EP4234550A2 - Methods and compounds for the treatment of genetic disease - Google Patents

Methods and compounds for the treatment of genetic disease Download PDF

Info

Publication number
EP4234550A2
EP4234550A2 EP23160417.4A EP23160417A EP4234550A2 EP 4234550 A2 EP4234550 A2 EP 4234550A2 EP 23160417 A EP23160417 A EP 23160417A EP 4234550 A2 EP4234550 A2 EP 4234550A2
Authority
EP
European Patent Office
Prior art keywords
optionally substituted
certain embodiments
alkyl
alkylene
terminus
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP23160417.4A
Other languages
German (de)
French (fr)
Other versions
EP4234550A3 (en
Inventor
Aseem Ansari
Pratik Shah
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Design Therapeutics Inc
Original Assignee
Design Therapeutics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Design Therapeutics Inc filed Critical Design Therapeutics Inc
Publication of EP4234550A2 publication Critical patent/EP4234550A2/en
Publication of EP4234550A3 publication Critical patent/EP4234550A3/en
Withdrawn legal-status Critical Current

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • A61K47/22—Heterocyclic compounds, e.g. ascorbic acid, tocopherol or pyrrolidones
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing three or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • chimeric heterocyclic polyamide compounds and compositions and their application as pharmaceuticals for the treatment of disease Disclosed herein are new chimeric heterocyclic polyamide compounds and compositions and their application as pharmaceuticals for the treatment of disease. Methods to modulate the expression of fxn in a human or animal subject are also provided for the treatment diseases such as Friedreich's ataxia.
  • the disclosure relates to the treatment of inherited genetic diseases characterized by underproduction of mRNA.
  • Friedreich's ataxia is an autosomal recessive neurodegenerative disorder caused by mutations in the fxn gene, which encodes the protein frataxin (FXN), a iron-binding mitochondrial protein involved in electron transport and metabolism.
  • FXN protein frataxin
  • a GAA trinucleotide repeat (from about 66 to over 1000 trinucleotides) is included in the first intron of fxn, and this hyperexpansion is responsible for the observed pathology. Hyperexpansion of the GAA repeats results in reduced expression of FXN.
  • Friedreich's ataxia is characterized by progressive degradation of the nervous system, particularly sensory neurons.
  • cardiomyocytes and pancreatic beta cells are susceptible to frataxin depletion. Symptoms usually present by age 18; however, later diagnoses of FA are not uncommon. FA patients develop neurodegeneration of the large sensory neurons and spinocerebellar tracts, as well as cardiomyopathy and diabetes mellitus.
  • FA Clinical symptoms of FA include ataxia, gait ataxia, muscle weakness, loss of upper body strength, loss of balance, lack of reflexes in lower limbs and tendons, loss of sensation, particularly to vibrations, impairment of position sense, impaired perception of temperature, touch, and pain, hearing and vision impairment, including disorted color vision and involuntary eye movements, irregular foot configuration, including pes cavus and inversion, hearing impairment, dysarthria, dysphagia, impaired breathing, scoliosis, diabetes, intolerance to glucose and carbohydrates, cardiac dysfunctions including hypertrophic cardiomyopathy, arrhythmia, myocardial fibrosis, and cardiac failure.
  • Currently there is no cure for FA with medical treatments being limited to surgical intervention for the spine and the heart, as well as therapy to assist with balance and coordination, motion, and speech.
  • This disclosure utilizes regulatory molecules present in cell nuclei that control gene expression.
  • Eukaryotic cells provide several mechanisms for controlling gene replication, transcription, and/or translation. Regulatory molecules that are produced by various biochemical mechanisms within the cell can modulate the various processes involved in the conversion of genetic information to cellular components.
  • Several regulatory molecules are known to modulate the production of mRNA and, if directed to fxn, would modulate the productionof fxn mRNA that causes Friedreich's ataxia , and thus reverse the progress of the disease.
  • the disclosure provides compounds and methods for recruiting a regulatory molecule into close proximity to fxn.
  • the compounds disclosed herein contain: (a) a recruiting moiety that will bind to a regulatory molecule, linked to (b) a DNA binding moiety that will selectively bind to fxn.
  • the compounds will counteract the expression of defective fxn in the following manner:
  • the mechanism set forth above will provide an effective treatment for Friedreich's ataxia, which is caused by the expression of defective fxn. Correction of the expression of the defective fxn gene thus represents a promising method for the treatment of Friedreich's ataxia.
  • the disclosure provides recruiting moieties that will bind to regulatory molecules.
  • Small molecule inhibitors of regulatory molecules serve as templates for the design of recruiting moieties, since these inhibitors generally act via noncovalent binding to the regulatory molecules.
  • the disclosure further provides for DNA binding moieties that will selectively bind to one or more copies of the GAA trinucleotide repeat that is characteristic of the defective fxn gene. Selective binding of the DNA binding moiety to fxn , made possible due to the high GAA count associated with the defective fxn gene, will direct the recruiting moiety into proximity of the gene, and recruit the regulatory molecule into position to up-regulate gene transcription.
  • the DNA binding moiety will comprise a polyamide segment that will bind selectively to the target GAA sequence.
  • Polyamides have been designed by Dervan and others that can selectively bind to selected DNA sequences. These polyamides sit in the minor groove of double helical DNA and form hydrogen bonding interactions with the Watson-Crick base pairs.
  • Polyamides that selectively bind to particular DNA sequences can be designed by linking monoamide building blocks according to established chemical rules. One building block is provided for each DNA base pair, with each building block binding noncovalently and selectively to one of the DNA base pairs: A/T, T/A, G/C, and C/G.. Following this guideline, trinucleotides will bind to molecules with three amide units, i.e. triamides.
  • these polyamides will orient in either direction of a DNA sequence, so that the 5'-GAA-3' trinucleotide repeat sequence of fxn can be targeted by polyamides selective either for GAA or for AAG.
  • polyamides that bind to the complementary sequence in this case, TTC or CTT, will also bind to the trinucleotide repeat sequence of fxn and can be employed as well.
  • longer DNA sequences can be targeted with higher specificity and/or higher affinity by combining a larger number of monoamide building blocks into longer polyamide chains.
  • the binding affinity for a polyamide would simply be equal to the sum of each individual monoamide / DNA base pair interaction.
  • longer polyamide sequences do not bind to longer DNA sequences as tightly as would be expected from a simple additive contribution.
  • the geometric mismatch between longer polyamide sequences and longer DNA sequences induces an unfavorable geometric strain that subtracts from the binding affinity that would be otherwise expected.
  • the disclosure therefore provides DNA moieties that comprise hexaamide or pentaamide subunits that are connected by flexible spacers.
  • the spacers alleviate the geometric strain that would otherwise decrease binding affinity of a larger polyamide sequence.
  • polyamide compounds that can bind to one or more copies of the trinucleotide repeat sequence GAA, and can modulate the expression of the defective fxn gene. Treatment of a subject with these compounds will counteract the expression of the defective fxn gene, and this can reduce the occurrence, severity, and/or frequency of symptoms associated with Friedreich's ataxia. Certain compounds disclosed herein will provide higher binding affinity and/or selectivity than has been observed previously for this class of compounds.
  • the transcription modulator molecule described herein represents an interface of chemistry, biology and precision medicine in that the molecule can be programmed to regulate the expression of a target gene containing nucleotide repeat GAA.
  • the transcription modulator molecule contains DNA binding moieties that will selectively bind to one or more copies of the GAA hexanucleotide repeat that is characteristic of the defective fxn gene.
  • the transcription modulator molecule also contains moieties that bind to regulatory proteins. The selective binding of the target gene will bring the regulatory protein into proximity to the target gene and thus downregulates transcription of the target gene.
  • the molecules and compounds disclosed herein provide higher binding affinity and selectivity than has been observed previously for this class of compounds and can be more effective in treating diseases associated with the defective fxn gene.
  • Treatment of a subject with these compounds will modulate the expression of the defective fxn gene, and this can reduce the occurrence, severity, or frequency of symptoms associated with ALS.
  • the transcription modulator molecules described herein recruits the regulatory molecule to modulate the expression of the defective fxn gene and effectively treats and alleviates the symptoms associated with diseases such as Friedreich ataxia.
  • the transcription modulator molecules disclosed herein possess useful activity for modulating the transcription of a target gene having one or more GAArepeats (e.g., fxn ), and may be used in the treatment or prophylaxis of a disease or condition in which the target gene (e.g., fxn ) plays an active role.
  • GAArepeats e.g., fxn
  • certain embodiments also provide pharmaceutical compositions comprising one or more compounds disclosed herein together with a pharmaceutically acceptable carrier, as well as methods of making and using the compounds and compositions. Certain embodiments provide methods for modulating the expression of fxn .
  • inventions provide methods for treating a jxn -mediated disorder in a patient in need of such treatment, comprising administering to said patient a therapeutically effective amount of a compound or composition according to the present disclosure. Also provided is the use of certain compounds disclosed herein for use in the manufacture of a medicament for the treatment of a disease or condition ameliorated by the modulation of the expression of fxn .
  • Some embodiments relate to a transcription modulator molecule or compound having a first terminus, a second terminus, and oligomeric backbone, wherein: a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to a nucleotide repeat sequence GAA; b) the second terminus comprises a protein-binding moiety binding to a regulatory molecule that modulates an expression of a gene comprising the nucleotide repeat sequence GAA; and c) the oligomeric backbone comprising a linker between the first terminus and the second terminus.
  • the second terminus is not a Brd4 binding moiety.
  • the compounds have structural Formula I: X-L-Y (I) or a salt thereof, wherein:
  • Certain compounds disclosed herein may possess useful activity for modulating the transcription of fxn, and may be used in the treatment and/or prophylaxis of a disease or condition in which fxn plays an active role.
  • certain embodiments also provide pharmaceutical compositions comprising one or more compounds disclosed herein together with a pharmaceutically acceptable carrier, as well as methods of making and using the compounds and compositions.
  • Certain embodiments provide methods for modulating the expression of fxn.
  • Other embodiments provide methods for treating a fxn- mediated disorder in a patient in need of such treatment, comprising administering to said patient a therapeutically effective amount of a compound or composition according to the present disclosure.
  • certain compounds disclosed herein for use in the manufacture of a medicament for the treatment of a disease or condition ameliorated by the modulation of the expression of fxn.
  • the regulatory molecule is chosen from a bromodomain-containing protein, a nucleosome remodeling factor (NURF), a bromodomain PHD finger transcription factor (BPTF), a teneleven translocation enzyme (TET), methylcytosine dioxygenase (TET1), a DNA demethylase, a helicase, an acetyltransferase, and a histone deacetylase ("HDAC").
  • NURF nucleosome remodeling factor
  • BPTF bromodomain PHD finger transcription factor
  • TET teneleven translocation enzyme
  • TET1 methylcytosine dioxygenase
  • DNA demethylase a helicase
  • HDAC histone deacetylase
  • the first terminus is Y
  • the second terminus is X
  • the oligomeric backbone is L
  • the compounds have structural Formula II: X-L-(Y 1 -Y 2 -Y 3 ) n -Y 0 (II) or a salt thereof, wherein:
  • the compounds of structural Formula II comprise a subunit for each individual nucleotide in the GAA repeat sequence.
  • each internal subunit has an amino (-NH-) group and a carboxy (-CO-) group.
  • the compounds of structural Formula II comprise amide (-NHCO-) bonds between each pair of internal subunits.
  • the compounds of structural Formula II comprise an amide (-NHCO-) bond between L and the leftmost internal subunit.
  • the compounds of structural Formula II comprise an amide bond between the rightmost internal subunit and the end subunit.
  • each subunit comprises a moiety that is independently chosen from a heterocycle and an aliphatic chain.
  • the heterocycle is a monocyclic heterocycle. In certain embodiments, the heterocycle is a monocyclic 5-membered heterocycle. In certain embodiments, each heterocycle contains a heteroatom independently chosen from N, O, or S. In certain embodiments, each heterocycle is independently chosen from pyrrole, imidazole, thiazole, oxazole, thiophene, and furan.
  • the aliphatic chain is a C 1-6 straight chain aliphatic chain. In certain embodiments, the aliphatic chain has structural formula -(CH 2 ) m -, for m chosen from 1, 2, 3, 4, and 5. In certain embodiments, the aliphatic chain is -CH 2 CH 2 -.
  • each subunit comprises a moiety independently chosen from -NH-benzopyrazinylene-CO-, -NH-phenylene-CO-, -NH-pyridinylene-CO-, -NH-piperidinylene-CO-, -NH-pyrimidinylene-CO-, -NH-anthracenylene-CO-, -NH-quinolinylene-CO-, and wherein Z is H, NH 2 , C 1-6 alkyl, C 1-6 haloalkyl or C 1-6 alkyl-NH 2 .
  • Py Im is Hp is Th is Pz is Nt is Tn is Nh is iNt is iIm is HpBi is ImBi is PyBi is Dp is -NH-benzopyrazinylene-CO- is -NH-phenylene-CO- is -NH-pyridinylene-CO- is -NH-piperidinylene-CO- is ,-NH-pyrazinylene-CO- is -NH-anthracenylene-CO- is and -NH-quinolinylene-CO- is In some embodiments, Py is Im is Hp is This
  • n is between 1 and 100, inclusive. In certain embodiments, n is between 1 and 50, inclusive. In certain embodiments, n is between 1 and 20, inclusive. In certain embodiments, n is between 1 and 10, inclusive. In certain embodiments, n is between 1 and 5, inclusive. In certain embodiments, n is an integer between 1 and 3, inclusive. In certain embodiments, n is chosen from 1 and 2. In certain embodiments, n is 1.
  • n is an integer between 1 and 5, inclusive.
  • n is an integer between 1 and 3, inclusive.
  • n is an integer between 1 and 2, inclusive.
  • n 1
  • L comprises a C 1-6 straight chain aliphatic segment.
  • L comprises (CH 2 OCH 2 ) m ; and m is an integer between 1 to 20, inclusive. In certain further embodiments, m is an integer between 1 to 10, inclusive. In certain further embodiments, m is an integer between 1 to 5, inclusive.
  • the compounds have structural Formula III: X-L-(Y 1 -Y 2 -Y 3 )-(W-Y 1 -Y 2 -Y 3 ) n -Y 0 (III) or a salt thereof, wherein:
  • Y 1 -Y 2 -Y 3 is:
  • Y 1 -Y 2 -Y 3 is:
  • Y 1 -Y 2 -Y 3 is Im-Py- ⁇ .
  • Y 1 -Y 2 -Y 3 is Im-Im- ⁇ .
  • each Y 1 -Y 2 -Y 3 is independently chosen from ⁇ -Py-Im and ⁇ -Im-Im.
  • At most one Y 1 -Y 2 -Y 3 is ⁇ -Im-Im.
  • n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula III, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula III, n is 1.
  • the compounds have structural Formula IV: X-L-(Y 1 -Y 2 -Y 3 )-V-(Y 4 -Y 5 -Y 6 )-Y 0 (IV) or a salt thereof, wherein:
  • n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula IV, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula IV, n is 1.
  • V is -HN-CH 2 CH 2 CH 2 -CO-.
  • At most one of Y 1 -Y 2 -Y 3 is ⁇ -Im-Im.
  • Y 1 -Y 2 -Y 3 is ⁇ -Py-Im.
  • n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula V, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula V, n is 1.
  • the compounds have structural Formula VI: or a salt thereof, wherein:
  • n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula VI, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula VI, n is 1.
  • the compounds have structural Formula VII: or a salt thereof, wherein:
  • n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula VII, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula VII, n is 1.
  • V is -(CH 2 ) a -NR 1 -(CH 2 ) 6 -, -(CH 2 ) a -, -(CH 2 ) a -O-(CH 2 ) b -, -(CH 2 ) a -CH(NHR 1 )-, -(CH 2 ) a -CH(NHR 1 )-, - ⁇ CR 2 R 3 ) a -, or -(CH 2 ) a -CH(NR 1 3 ) + -(CH 2 ) b -, wherein each a is independently an integer between 2 and 4; R 1 is H, an optionally substituted C 1-6 alkyl, an optionally substituted C 3-10 cycloalkyl, an optionally substituted C 6-10 aryl, an optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; each R 2 and R 3 are independently H, halogen,
  • R 1 is H. In some embodiments, R 1 is C 1-6 alkyl optionally substituted by 1-3 substituents selected from -C(O)-phenyl.
  • V is -(CR 2 R 3 )-(CH 2 )a- or -(CH 2 )a-(CR 2 R 3 )-(CH 2 ) b -, wherein each a is independently 1-3, b is 0-3, and each R 2 and R 3 are independently H, halogen, OH, NHAc, or C 1-4 alky.
  • V is -(CH 2 )- CH(NH 3 ) + -(CH 2 )- or -(CH 2 )-CH 2 CH(NH 3 ) + -.
  • the compounds of the present disclosure bind to the GAAof fxn and recruit a regulatory moiety to the vicinity of fxn.
  • the regulatory moiety due to its proximity to the gene, will be more likely to modulate the expression of fxn .
  • any compound disclosed above including compounds of Formulas 1 - VII, are singly, partially, or fully deuterated. Methods for accomplishing deuterium exchange for hydrogen are known in the art.
  • two embodiments are "mutually exclusive" when one is defined to be something which is different than the other.
  • an embodiment wherein two groups combine to form a cycloalkyl is mutually exclusive with an embodiment in which one group is ethyl the other group is hydrogen.
  • an embodiment wherein one group is CH 2 is mutually exclusive with an embodiment wherein the same group is NH.
  • the compounds of the present disclosure bind to the GAA of fxn and recruit a regulatory moiety to the vicinity of fxn .
  • the regulatory moiety due to its proximity to the gene, will be more likely to modulate the expression of fxn .
  • the compounds of the present disclosure provide a polyamide sequence for interaction of a single polyamide subunit to each base pair in the GAA repeat sequence.
  • the compounds of the present disclosure provide a turn component V, in order to enable hairpin binding of the compound to the GAA, in which each nucleotide pair interacts with two subunits of the polyamide.
  • the compounds of the present disclosure provide more than one copy of the polyamide sequence for noncovalent binding to the fxn, and the individual polyamide sequences in this compound are linked by a spacer W, as defined above.
  • the spacer W allows this compound to adjust its geometry as needed to alleviate the geometric strain that otherwise affects the noncovalent binding of longer polyamide sequences.
  • the compounds of the present disclosure provide a polyamide sequence for interaction of a single polyamide subunit to each base pair in the GAA repeat sequence.
  • the compounds of the present disclosure provide a turn component (e.g, aliphatic amino acid moiety), in order to enable hairpin binding of the compound to the GAA, in which each nucleotide pair interacts with two subunits of the polyamide.
  • the compounds of the present disclosure are more likely to bind to the repeated GAA of fxn than to GAA elsewhere in the subject's DNA, due to the high number of GAA repeats associated with fxn.
  • the compounds of the present disclosure provide more than one copy of the polyamide sequence for noncovalent binding to GAA. In one aspect, the compounds of the present disclosure bind to fxn with an affinity that is greater than a corresponding compound that contains a single polyamide sequence.
  • the compounds of the present disclosure provide more than one copy of the polyamide sequence for noncovalent binding to the GAA, and the individual polyamide sequences in this compound are linked by a spacer W, as defined above.
  • the spacer W allows this compound to adjust its geometry as needed to alleviate the geometric strain that otherwise affects the noncovalent binding of longer polyamide sequences.
  • the DNA recognition or binding moiety binds in the minor groove of DNA.
  • the DNA recognition or binding moiety comprises a polymeric sequence of monomers, wherein each monomer in the polymer selectively binds to a certain DNA base pair.
  • the DNA recognition or binding moiety comprises a polyamide moiety.
  • the DNA recognition or binding moiety comprises a polyamide moiety comprising heteroaromatic monomers, wherein each heteroaromatic monomer binds noncovalently to a specific nucleotide, and each heteroaromatic monomer is attached to its neighbor or neighbors via amide bonds.
  • the DNA recognition moiety binds to a sequence comprising at least 1000 pentanucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 500 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 200 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 100 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 50 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 20 trinucleotide repeats.
  • the compounds comprise a cell-penetrating ligand moiety.
  • the cell-penetrating ligand moiety is a polypeptide.
  • the cell-penetrating ligand moiety is a polypeptide containing fewer than 30 amino acid residues.
  • polypeptide is chosen from any one of SEQ ID NO. 1 to SEQ ID NO. 37, inclusive.
  • the form of the polyamide selected can vary based on the target gene.
  • the first terminus can include a polyamide selected from the group consisting of a linear polyamide, a hairpin polyamide, a H-pin polyamide, an overlapped polyamide, a slipped polyamide, a cyclic polyamide, a tandem polyamide, and an extended polyamide.
  • the first terminus comprises a linear polyamide.
  • the first terminus comprises a hairpin polyamide.
  • the binding affinity between the polyamide and the target gene can be adjusted based on the composition of the polyamide.
  • the polyamide is capable of binding the DNA with an affinity of less than about 600 nM, about 500 nM, about 400 nM, about 300 nM, about 250 nM, about 200 nM, about 150 nM, about 100 nM, or about 50nM.
  • the polyamide is capable of binding the DNA with an affinity of less than about 300 nM.
  • the polyamide is capable of binding the DNA with an affinity of less than about 200 nM.
  • the polyamide is capable of binding the DNA with an affinity of greater than about 200 nM, about 150 nM, about 100 nM, about 50 nM, about 10 nM, or about 1 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity in the range of about 1-600 nM, 10-500 nM, 20-500 nM, 50-400 nM, or 100-300 nM.
  • the binding affinity between the polyamide and the target DNA can be determined using a quantitative footprint titration experiment.
  • the experiment involve measuring the dissociation constant Kd of the polyamide for target sequence at either 24° C. or 37° C., and using either standard polyamide assay solution conditions or approximate intracellular solution conditions.
  • the binding affinity between the regulatory protein and the ligand on the second terminus can be determined using an assay suitable for the specific protein.
  • the experiment involve measuring the dissociation constant Kd of the ligand for protein and using either standard protein assay solution conditions or approximate intracellular solution conditions.
  • the first terminus comprises -NH-Q-C(O)-, wherein Q is an optionally substituted C 6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene group. In some embodiments, Q is an optionally substituted C 6-10 arylene group or optionally substituted 5-10 membered heteroarylene group. In some embodiments, Q is an optionally substituted 5-10 membered heteroarylene group.
  • the 5-10 membered heteroarylene group is optionally substituted with 1-4 substituents selected from H, OH, halogen, C 1-10 alkyl, NO 2 , CN, NR'R", C 1-6 haloalkyl, C 1-6 alkoxyl, C 1-6 haloalkoxy, (C 1-6 alkoxy)C 1-6 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-7 carbocyclyl, 4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, (C 3-7 carbocyclyl)C 1-6 alkyl, (4-10 membered heterocyclyl)C 1-6 alkyl, (C 6-10 aryl)C 1-6 alkyl, (C 6-10 aryl)C 1-6 alkoxy, (5-10 membered heteroaryl)C 1-6 alkyl, (C 3-7 carbocyclyl)-amine, (4-10 membered heterocyclyl)amine
  • the first terminus comprises at least three aromatic carboxamide moieties selected to correspond to the nucleotide repeat sequence GAA and at least one aliphatic amino acid residue chosen from the group consisting of glycine, ⁇ -alanine, ⁇ -aminobutyric acid, 2,4-diaminobutyric acid, and 5-aminovaleric acid.
  • the first terminus comprises at least one ⁇ -alanine subunit.
  • the monomer element is independently selected from the group consisting of optionally substituted pyrrole carboxamide monomer, optionally substituted imidazole carboxamide monomer, optionally substituted C-C linked heteromonocyclic/heterobicyclic moiety, and ⁇ -alanine.
  • the first terminus can comprise a structure of Formula (A-2): wherein:
  • the integers p and q are 2 ⁇ p+q ⁇ 20. In some embodiments, p is in the range of about 2 to 10. In some embodiments, p is in the range of about 4 to 8. In some embodiments, q is in the range of about 2 to 10. In some embodiments, q is in the range of about 4 to 8.
  • L 2a is-C 2-8 alkylene-CH, and wherein each m and n is independently an integer in the range of 0 to 10. In certain embodiments, L 2a is In some embodiments, L 2a is -C 2-8 alkylene-CH. In some embodiments, L 2a is wherein (m+n) is in the range of about 1 to 4. In some embodiments, L 2a is and (m+n) is in the range of about 2 to 5. In some embodiments, L 2a is wherein (m+n) is in the range of about 1 to 6.
  • the integers p 1 and q 1 are 2 ⁇ p 1 + q 1 ⁇ 20.
  • L 1a is a bond.
  • L 1a is a C 1-6 alkylene.
  • L 1a is -NH-C 1-6 alkylene-C(O)-.
  • L 1a is - N(CH 3 )-C 1-6 alkylene-.
  • L 1a is -O-C 0-6 alkylene-.
  • L 3a is a bond. In some embodiments, L 3a is C 1-6 alkylene. In some embodiments, L 3a is -NH-C 1-6 alkylene-C(O)-. In some embodiments, L 3a is -N(CH 3 )-C 1-6 alkylene C(O)-. In some embodiments, L 3a is -O-C 0-6 alkylene. In some embodiments, L 3a is -(CH 2 ) a -NR a -(CH 2 ) b -. In some embodiments, L 3a is -(CH 2 ) a -O-(CH 2 ) b -.
  • L 3a is -(CH 2 ) a -CH(NHR a )-. In some embodiments, L 3a is -(CH 2 ) a -CH(NHR a )-. In some embodiments, L 3a is -(CR 1a R 1b ) a -. In some embodiments, L 3a is -(CH 2 ) a -CH(NR a R b )-(CH 2 ) b -.
  • At least one A is NH and at least one A is C(O). In some embodiments, for Formula (A-1) to (A-4), at least two A is NH and at least two A is C(O). In some embodiments, when M is a bicyclic ring, A is a bond. In some embodiments, at least one A is a phenylene optionally substituted with one or more alkyl. In some embodiments, at least one A is thiophenylene optionally substituted with one or more alkyl. In some embodiments, at least one A is a furanylene optionally substituted with one or more alkyl.
  • each M in [A-M] of Formula (A-1) to (A-4) is C 6-10 arylene group, 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or C 1-6 alkylene; each optionally substituted by 1-3 substituents selected from H, OH, halogen, C 1-10 alkyl, NO 2 , CN, NR a R b , C 1-6 haloalkyl, -C 1-6 alkoxyl, C 1-6 haloalkoxy, (C 1-6 alkoxy)C 1-6 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-7 carbocyclyl, 44-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, -(C 3-7 carbocyclyl)C 1-6 alkyl, (4-10 membered heterocyclyl)C 1-6 alkyl, (C 6-10 aryl)C 1-6 alkylene; each
  • each M in [A-M] of Formula (A-1) to (A-3) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N or a C 1-6 alkylene, and the heteroarylene or the a C 1-6 alkylene is optionally substituted with 1-3 substituents selected from OH, halogen, C 1-10 alkyl, NO 2 , CN, NR a R b , C 1-6 haloalkyl, -C 1-6 alkoxyl, C 1-6 haloalkoxy, C 3-7 carbocyclyl, 4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, -SR', COOH, or CONR a R b ; wherein each R a and R b are independently H, C 1-10 alkyl, C 1-10 haloalkyl, -C 1-10 alkoxyl.
  • each R in [A-R] of Formula (A-1) to (A-3) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N, and the heteroarylene is optionally substituted with 1-3 substituents selected from OH, C 1-6 alkyl, halogen, and C 1-6 alkoxyl.
  • At least one M is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least one M is a pyrrole optionally subsituted with one or more C 1-10 alkyl.
  • at least one M is a immidazole optionally subsituted with one or more C 1-10 alkyl.
  • at least one M is a C 2-6 alkylene optionally substituted with one or more C 1-10 alkyl.
  • At least one M is a pyrrole optionally subsituted with one or more C 1-10 alkyl.
  • at least one M is a bicyclic heteroarylene or arylene.
  • at least one M is a phenylene optionally subsituted with one or more C 1-10 alkyl.
  • at least one M is a benzimmidazole optionally subsituted with one or more C 1-10 alkyl.
  • the first terminus comprises a structure of Formula (A-4): wherein:
  • the first terminus comprises a structure of Formula (A-4a) or (A-4b): or wherein:
  • L 1c is C 1-10 alkylene, or In certain embodiments, L 1c is C 3-8 alkylene. In certain embodiments, L 1c is and wherein 2 ⁇ m+n ⁇ 10. In some embodiments, L 1c is C 2-8 alkylene. In some embodiments, L 1c is C 3-8 alkylene. In some embodiments, L 1c is C 4-8 alkylene. In some embodiments, L 1c is C 3 alkylene, C 4 alkylene, C 5 alkylene, C 6 alkylene, C 7 alkylene, C 8 alkylene, or C 9 alkylene.
  • (m+n) is 3, 4, 5, 6, 7, 8, or 9. In certain embodiments, m is in the range of 3 to 8. In certain embodiments, m is 3, 4, 5, 6, 7, 8, or 9.
  • M q is a five to 10 membered heteroaryl ring comprising at least one nitrogen; Q q is a five to 10 membered heteroaryl ring comprising at least one nitrogen; and M q is linked to Q q through L 1c .
  • M q is a five membered heteroaryl ring comprising at least one nitrogen; Q q is a five membered heteroaryl ring comprising at least one nitrogen; M q is linked to Q q through L 1c , and L 1c is attached to the nitrogen atom on M q and L 1c is attached to the nitrogen atom on Q q .
  • each M 1 through M p is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C 1-6 alkylene.
  • At least one M of M 1 through M p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least two M of M 1 through M p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least three, four, five, or six M of M 1 through M p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • At least one of M 1 through M p is a pyrrole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of M 1 through M p is a immidazole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of M 1 through M p is a C 2-6 alkylene optionally substituted with one or more C 1-10 alkyl. In some embodiments, at least one of M 1 through M p is a phenyl optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of M 1 through M p is a bicyclic heteroarylene or arylene.
  • At least one of M 1 through M p is a phenylene optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of M 1 through M p is a benzimmidazole optionally subsituted with one or more C 1-10 alkyl.
  • each Q 1 to Q p is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C 1-6 alkylene.
  • At least one Q of Q 1 through Q p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least two Q of Q 1 through Q p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least three, four, five, or six Q of Q 1 through Q p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • At least one of Q 1 through Q p is a pyrrole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q 1 through Q p is a immidazole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q 1 through Q p is a C 2-6 alkylene optionally substituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q 1 through Q p is a phenyl optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q 1 through Q p is a bicyclic heteroarylene or arylene.
  • At least one of Q 1 through Q p is a phenylene optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q 1 through Q p is a benzimmidazole optionally subsituted with one or more C 1-10 alkyl.
  • At least one of A 2 through A p is NH and at least one of A 2 through A p is C(O). In some embodiments, at least two of A 2 through A p is NH and at least two of A 2 through A p is C(O). In some embodiments, when one of M 2 through M p is a bicyclic ring, the adjacent A is a bond. In some embodiments, one of A 2 through A p is a phenylene optionally substituted with one or more alkyl. In some embodiments, one of A 2 through A p is thiophenylene optionally substituted with one or more alkyl.
  • one of A 2 through A p is a furanylene optionally substituted with one or more alkyl.
  • one of A 2 through A p is -NH-C(O)-NH-.
  • one of A 2 through A p is -N(CH 3 )-C 1-6 alkylene.
  • one of A 2 through A p is In some embodiments, one of A 2 through A p is -NH- C 1-6 alkylene-NH-. In some embodiments, one of A 2 through A p is -O-C 1-6 alkylene-O-.
  • At least one T of T 2 through T p is NH and at least one of T of T 2 through T p is C(O). In some embodiments, at least two T of T 2 through T p is NH and at least two T of T 2 through T p is C(O). In some embodiments, when one Q of Q 2 through Q p is a bicyclic ring, the adjacent T is a bond. In some embodiments, one T of T 2 through T p is a phenylene optionally substituted with one or more alkyl. In some embodiments, one T of T 2 through T p is thiophenylene optionally substituted with one or more alkyl.
  • one T of T 2 through T p is a furanylene optionally substituted with one or more alkyl.
  • one T of T 2 through T p is -NH-C(O)-NH-.
  • one T of T 2 through T p is -N(CH 3 )-C 1-6 alkylene.
  • one T of T 2 through T p is In some embodiments, one T of T 2 through T p is -NH- C 1-6 alkylene-NH-. In some embodiments, one T of T 2 through T p is -O-C 1-6 alkylene-O-.
  • each A 1 , T 1 , E 1 , and E 2 are independently -A E -G, and each A E is independently absent or NHCO. In certain embodiments, each A 1 , T 1 , E 1 , and E 2 are independently -A E -G and each A E is independently NHCO.
  • each end group G independently comprises a NH or CO group.
  • each R a and R b are independently H or C 1-6 alkyl.
  • at least one of the end groups is H.
  • at least two of the end groups are H.
  • at least one of the end groups is H.
  • At least one of the end groups is -NH-5-10 membered heteroaryl ring optionally substituted with one or more alkyl or -CO-5-10 membered heteroaryl ring optionally substituted with one or more alkyl.
  • each E 1 independently comprises an optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted imidazole containing moiety, or optionally substituted amine.
  • each E 2 independently comprises an optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted imidazole containing moiety, or optionally substituted amine
  • each E 1 and E 2 independently comprises a moiety selected from the group consisting of optionally substituted N-methylpyrrole, optionally substituted N-methylimidazole, optionally substituted benzimidazole moiety, and optionally substituted 3-(dimethylamino)propanamidyl.
  • each E 1 and E 2 independently comprises thiophene, benzothiophene, C-C linked benzimidazole/thiophene-containing moiety, or C-C linked hydroxybenzimidazole/thiophene-containing moiety.
  • each E 1 and E 2 independently also comprises NH or CO group.
  • each E 1 or E 2 independently comprises a moiety selected from the group consisting of isophthalic acid; phthalic acid; terephthalic acid; morpholine; N,N-dimethylbenzamide; N,N-bis(trifluoromethyl)benzamide; fluorobenzene; (trifluoromethyl)benzene; nitrobenzene; phenyl acetate; phenyl 2,2,2-trifluoroacetate; phenyl dihydrogen phosphate; 2H-pyran; 2H-thiopyran; benzoic acid; isonicotinic acid; and nicotinic acid; wherein one, two, or three ring members in any of the end-group candidates can be independently substituted with C, N, S or O; and where any one, two, three, four or five of the hydrogens bound to the ring can be substituted with R 3a , wherein R 5 may be independently selected from H, OH,
  • the first terminus comprises the structure of Formula (A-5a) or Formula (A-5b): A 1a -NH-Q 1 -C(O)-NH-Q 2 -C(O)-NH-Q 3 -C(O)... -NH-Q p-1 C(O)-NH-C(O)NH-G (A-Sa) or T 1a -C(O)-Q 1 -NH-C(O)-Q 2 NH-C(O)-Q 3 -NH-... -C(O)-Q p-1 NH-C(O)-Q p -NHC(O)-G (A-5b) wherein:
  • the first terminus comprises the structure of Formula (A-5c): wherein:
  • the first terminus comprises the structure of Formula (A-5c) or (A-5d): or wherein:
  • L a is a C 2-8 alkylene.
  • L 6 is C 3-8 alkylene.
  • L a is and wherein 2 ⁇ m+n ⁇ 10.
  • L a is C 4-8 alkylene.
  • L a is C 3-7 alkylene.
  • L a is C 3 alkylene, C 4 alkylene, C 5 alkylene, C 6 alkylene, C 7 alkylene, C 8 alkylene, or C 9 alkylene.
  • Q a q is a five to 10 membered heteroaryl ring comprising at least one nitrogen
  • Q b q' is a five to 10 membered heteroaryl ring comprising at least one nitrogen
  • Q a q is linked to Q b r through L a .
  • Q a q is a five membered heteroaryl ring comprising at least one nitrogen
  • Q b r is a five membered heteroaryl ring comprising at least one nitrogen
  • Q a q is linked to Q b r through L a
  • L a is attached to the nitrogen atom on Q a q
  • L 1c is attached to the nitrogen atom on Q b r .
  • each Q a 1 through Q a p is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C 1-6 alkylene.
  • At least one Q of Q a 1 through Q a p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least two Q of Q a 1 through Q a p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least three, four, five, or six Q of Q a 1 through Q a p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • At least one Q of Q a 1 through Q a p is a pyrrole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q of Q a 1 through Q a p is a immidazole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one Q of Q a 1 through Q a p is a C 2-6 alkylene optionally substituted with one or more C 1-10 alkyl. In some embodiments, at least one Q of Q a 1 through Q a p is a phenyl optionally subsituted with one or more C 1-10 alkyl.
  • At least one Q of Q a 1 through Q a p is a bicyclic heteroarylene or arylene. In some embodiments, at least one Q of Q a 1 through Q a p is a phenylene optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one Q of Q a 1 through Q a p is a benzimmidazole optionally subsituted with one or more C 1-10 alkyl.
  • each Q b 1 through Q b p is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C 1-6 alkylene.
  • At least one Q of Q b 1 through Q b p' is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least two Q of Q b 1 through Q b p' is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • at least three, four, five, or six Q of Q b 1 through Q b p' is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C 1-10 alkyl.
  • At least one of Q b 1 through Q b p' is a pyrrole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q b 1 through Q b p' is a immidazole optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q b 1 through Q b p' is a C 2-6 alkylene optionally substituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q b 1 through Q b p' is a phenyl optionally subsituted with one or more C 1-10 alkyl.
  • At least one of Q b 1 through Qb p' is a bicyclic heteroarylene or arylene. In some embodiments, at least one of Q b 1 through Q b p' is a phenylene optionally subsituted with one or more C 1-10 alkyl. In some embodiments, at least one of Q b 1 through Q b p' is a benzimmidazole optionally subsituted with one or more C 1-10 alkyl.
  • each R a and R b are independently H or C 1-6 alkyl.
  • at least one of the end groups is 5-10 membered heteroaryl optionally substituted with C 1-6 alkyl, COOH, or OH.
  • at least two of the end groups are 5-10 membered heteroaryl optionally substituted with C 1-6 alkyl, COOH, or OH.
  • at least one of the end groups is 5-10 membered heteroaryl optionally substituted with C 1-6 alkyl, COOH, or OH.
  • at least one of the end groups is 5-10 membered heteroaryl ring optionally substituted with one or more alkyl.
  • a E is absent. In some embodiments, A E is NHCO-.
  • the first terminus comprises at least one C 3-5 achiral aliphatic or heteroaliphatic amino acid.
  • the first terminus comprises one or more subunits selected from the group consisting of optionally substituted pyrrole, optionally substituted imidazole, optionally substituted thiophene, optionally substituted furan, optionally substituted beta-alanine, ⁇ -aminobutyric acid, (2-aminoethoxy)-propanoic acid, 3((2-aminoethyl)(2-oxo-2-phenyl-1 ⁇ 2 -ethyl)amino)-propanoic acid, or dimethylaminopropylamide monomer.
  • the first terminus comprises a polyamide having the structure of Formula (A-6): wherein:
  • each M 1 in [A 1 -M 1 ] of Formula (A-6) is a C 6-10 arylene group, 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or C 1-6 alkylene; each optionally substituted by 1-3 substituents selected from H, OH, halogen, C 1-10 alkyl, NO 2 , CN, NR'R", C 1-6 haloalkyl, - C 1-6 alkoxyl, C 1-6 haloalkoxy, (C 1-6 alkoxy)C 1-6 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-7 carbocyclyl, 4-10 membered heterocyclyl4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, -(C 3-7 carbocyclyl)C 1-6 alkyl, (4-10 membered heterocyclyl4-10 membered heterocyclyl)C 1-6 alkyl,
  • each R 1 in [A 1 -R 1 ] of Formula (A-6) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N or a C 1-6 alkylene, and the heteroarylene or the a C 1-6 alkylene is optionally substituted with 1-3 substituents selected from OH, halogen, C 1-10 alkyl, NO 2 , CN, NR'R", C 1-6 haloalkyl, -C 1-6 alkoxyl, C 1-6 haloalkoxy, C 3-7 carbocyclyl, 4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, -SR, COOH, or CONRR"; wherein each R' and R" are independently H, C 1-10 alkyl, C 1-10 haloalkyl, -C 1-10 alkoxyl.
  • each R 1 in [A 1 -R 1 ] of Formula (A-6) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N, and the heteroarylene is optionally substituted with 1-3 substituents selected from OH, C 1-6 alkyl, halogen, and C 1-6 alkoxyl.
  • the first terminus has a structure of Formula (A-7): or a salt thereof, wherein:
  • m 1 is 3, and X 1 , Y 1 , and Z 1 in the first unit is respectively CH, N(CH 3 ), and CH; X 1 , Y 1 , and Z 1 in the second unit is respectively CH, N(CH 3 ), and N; and X 1 , Y 1 , and Z 1 in the third unit is respectively CH, N(CH 3 ), and N.
  • m 3 is 1, and X 2 , Y 2 , and Z 2 in the first unit is respectively CH, N(CH 3 ), and CH.
  • m 5 is 2, and X 3 , Y 3 , and Z 3 in the first unit is respectively CH, N(CH 3 ), and N; X 3 , Y 3 , and Z 3 in the second unit is respectively CH, N(CH 3 ), and N.
  • m 7 is 2, and X 4 , Y 4 , and Z 4 in the first unit is respectively CH, N(CH 3 ), and CH; X 4 , Y 4 , and Z 4 in the second unit is respectively CH, N(CH 3 ), and CH.
  • each m 2 , m 4 and m 6 are independently 0 or 1.
  • each of the X 1 , Y 1 , and Z 1 in each m 1 unit are independently selected from CH, N, or N(CH 3 ).
  • each of the X 2 , Y 2 , and Z 2 in each m 3 unit are independently selected from CH, N, or N(CH 3 ).
  • each of the X 3 , Y 3 , and Z 3 in each m 5 unit are independently selected from CH, N, or N(CH 3 ).
  • each of the X 4 , Y 4 , and Z 4 in each m 7 unit are independently selected from CH, N, or N(CH 3 ).
  • each Z 1 in each m 1 unit is independently selected from CR 4 or NR 5 .
  • each Z 2 in each m 3 unit is independently selected from CR 4 or NR 5 .
  • each Z 3 in each m 5 unit is independently selected from CR 4 or NR 5 .
  • each Z 4 in each m 7 unit is independently selected from CR 4 or NR 5 .
  • R 4 is H, CH 3 , or OH.
  • R 5 is H or CH 3 .
  • the sum of m 2 , m 4 and m 6 is between 1 and 6. In some embodiments, for formula (A-7), the sum of m 2 , m 4 and m 6 is between 2 and 6. In some embodiments, for Formula (A-7), the sum of m 1 , m 3 , m 5 and m 7 is between 2 and 10. In some embodiments, the sum of m 1 , m 3 , m 5 and m 7 is between 3 and 8. In some embodiments, for Formula (A-7), (m 1 + m 2 + m 3 + m 4 + m 5 + m 6 + m 7 ) is between 3 and 12. In some embodiments, (m 1 + m 2 + m 3 + m 4 + m 5 + m 6 + m 7 ) is between 4 and 10.
  • the first terminus comprises at least one beta-alanine moiety. In some embodiments, for Formula (A-1) to (A-7), the first terminus comprises at least two beta-alanine moieties. In some embodiments, for Formula (A-1) to (A-7), the first terminus comprises at least three or four beta-alanine moieties.
  • the first terminus has the structure of Formula (A-8): or a salt thereof, wherein:
  • the sum of n 2 , n 4 , n 7 and n 9 is between 1 and 6. In some embodiments, for Formula (A-8), the sum of n 2 , n 4 , n 7 and n 9 is between 2 and 6. In some embodiments, for Formula (A-8), the sum of n 1 , n 3 , n 5 , n 6 , n 8 and n 10 is between 3 and 13. In some embodiments, the sum of n 1 , n 3 , n 5 , n 6 , n 8 and n 10 is between 4 and 10.
  • (n 1 + n 2 + n 3 + n 4 + n 5 + n 6 + n 7 + n 8 + n 9 + n 10 ) is between 3 and 12. In some embodiments, (n 1 + n 2 + n 3 + n 4 + n 5 + n 6 + n 7 + n 8 + n 9 + n 10 ) is between 4 and 10.
  • n 1 is 3, and X 1 ', Y 1' , and Z 1' in the first unit is respectively CH, N(CH 3 ), and CH; X 1' , Y 1' , and Z 1' in the second unit is respectively CH, N(CH 3 ), and N; and X 1 ', Y 1' , and Z 1' in the third unit is respectively CH, N(CH 3 ), and N.
  • n 3 is 1, and X 2' , Y 2' , and Z 2' in the first unit is respectively CH, N(CH 3 ), and CH.
  • n 5 is 2, and X 3' , Y 3' , and Z 3' in the first unit is respectively CH, N(CH 3 ), and N; X 3' , Y 3' , and Z 3' in the second unit is respectively CH, N(CH 3 ), and N.
  • n 6 is 2, and X 4' , Y 4' , and Z 4' in the first unit is respectively CH, N(CH 3 ), and N; X 4' , Y 4' , and Z 4' in the second unit is respectively CH, N(CH 3 ), and N.
  • the X 1 ', Y 1' , and Z 1' in each n 1 unit are independently selected from CH, N, or N(CH 3 ).
  • the X 2' , Y 2' , and Z 2' in each n 3 unit are independently selected from CH, N, or N(CH 3 ).
  • the X 3' , Y 3' , and Z 3' in each n 5 unit are independently selected from CH, N, or N(CH 3 ).
  • the X 4' , Y 4' , and Z 4' in each n 6 unit are independently selected from CH, N, or N(CH 3 ).
  • the X 5' , Y 3 , and Z 5' in each n 8 unit are independently selected from CH, N, or N(CH 3 ).
  • the X 6' , Y 6' , and Z 6' in each n 10 unit are independently selected from CH, N, or N(CH 3 ).
  • each Z 1' in each n 1 unit is independently selected from CR 4 or NR 5 .
  • each Z 2' in each n 3 unit is independently selected from CR 4 or NR 5 .
  • each Z 3' in each n 5 unit is independently selected from CR 4 or NR 5 .
  • each Z 4' in each n 6 unit is independently selected from CR 4 or NR 5 .
  • each Z 5' in each n 8 unit is independently selected from CR 4 or NR 5 .
  • each Z 6' in each n 10 unit is independently selected from CR 4 or NR 5 .
  • R 4 is H, CH 3 , or OH.
  • R 3 is H or CH 3 .
  • the first terminus has the structure of Formula (A-9): or a salt thereof, wherein:
  • the first terminus comprises a polyamide having the structure of Formula (A-10): wherein:
  • each R 4 is independently H, -OH, halogen, C 1-6 alkyl, C 1-6 alkoxyl; and each R 2 is independently H, C 1-6 alkyl or C 1-6 alkylamine.
  • each R 4 is selected from the group consisting of H, COH, Cl, NO, N-acetyl, benzyl, C 1-6 alkyl, C 1-6 alkoxyl, C 1-6 alkenyl, C 1-6 alkynyl, C 1-6 alkylamine, -C(O)NH-(CH 2 ) 1-4 -C(O)NH -(CH 2 ) 1-4 -NR a R b ; and each R a and R b are independently hydrogen or C 1-6 alkyl.
  • R 5 is independently selected from the group consisting of H, C 1-6 alkyl, and C 1-6 alkylNH 2 , preferably H, methyl, or isopropyl.
  • R 4 in Formula (A-7) to (A-8) is independently selected from H, OH, C 1-6 alkyl, halogen, and C 1-6 alkoxyl. In some embodiments, R 4 in Formula (A-7) to (A-8) is selected from H, OH, halogen, C 1-10 alkyl, NO 2 , CN, NR'R", C 1-6 haloalkyl, -C 1-6 alkoxyl, C 1-6 haloalkoxy, (C 1-6 alkoxy)C 1-6 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-7 carbocyclyl, 4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, -(C 3-7 carbocyclyl)C 1-6 alkyl, (4-10 membered heterocyclyl)C 1-6 alkyl, (C 6-10 aryl)C 1-6 alkyl, (C 6-10 aryl)C 1-6 1-6 alky
  • R 4 in Formula (A-7) to (A-8) is selected from O, S, and N or a C 1-6 alkylene, and the heteroarylene or the a C 1-6 alkylene is optionally substituted with 1-3 substituents selected from OH, halogen, C 1-10 alkyl, NO 2 , CN, NR'R", C 1-6 haloalkyl, -C 1-6 alkoxyl, C 1-6 haloalkoxy, C 3-7 carbocyclyl, 4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, -SR, COOH, or CONR'R"; wherein each R' and R" are independently H, C 1-10 alkyl, C 1-10 haloalkyl, -C 1-10 alkoxyl.
  • each E, E 1 and E 2 independently are optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted immidazole containing moiety, and optionally substituted amine.
  • each E, E 1 and E 2 are independently selected from the group consisting of N-methylpyrrole, N-methylimidazole, benzimidazole moiety, and 3-(dimethylamino)propanamidyl, each group optionally substituted by 1-3 substituents selected from the group consisting of H, OH, halogen, C 1-10 alkyl, NO 2 , CN, NR'R", C 1-6 haloalkyl, -C 1-6 alkoxyl, C 1-6 haloalkoxy, (C 1-6 alkoxy)C 1-6 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-7 carbocyclyl, 4-10 membered heterocyclyl, C 6-10 aryl, 5-10 membered heteroaryl, amine, acyl, C-carboxy, O-carboxy, C-amido, N-amido, S-sulfonamido, N-sulfona
  • each E 1 and E 2 independently comprises thiophene, benzthiophene, C-C linked benzimidazole/thiophene-containing moiety, or C-C linked hydroxybenzimidazole/thiophene-containing moiety, wherein each R' and R" are independently H, C 1-10 alkyl, C 1-10 haloalkyl, -C 1-10 alkoxyl..
  • each E, E 1 or E 2 are independently selected from the group consisting of isophthalic acid; phthalic acid; terephthalic acid; morpholine; N,N-dimethylbenzamide; N,N-bis(trifluoromethyl)benzamide; fluorobenzene; (trifluoromethyl)benzene; nitrobenzene; phenyl acetate; phenyl 2,2,2-trifluoroacetate; phenyl dihydrogen phosphate; 2H-pyran; 2H-thiopyran; benzoic acid; isonicotinic acid; and nicotinic acid; wherein one, two or three ring members in any of these end-group candidates can be independently substituted with C, N, S or O; and where any one, two, three, four or five of the hydrogens bound to the ring can be substituted with R 5 , wherein R 5 may be independently selected for any substitution from H, OH, halogen, C 1-10 alkyl, NO 2
  • the DNA recognition or binding moiety can include one or more subunits selected from the group consisting of: -NH-benzopyrazinylene-CO-, -NH-phenylene-CO-, -NH-pyridinylene-CO-, -NH-piperidinylene-CO-, -NH-pyrimidinylene-CO-, -NH-anthracenylene-CO-, -NH-quinolinylene-CO-, and wherein Z is H, NH 2 , C 1-6 alkyl, or C 1-6 alkylNH 2.
  • the first terminus comprises one or more subunits selected from the group consisting of optionally substituted N-methylpyrrole, optionally substituted N-methylimidazole, and ⁇ -alanine ( ⁇ ).
  • the first terminus does not have a structure of
  • the first terminus in the molecules described herein has a high binding affinity to a sequence having multiple repeats of GAA and binds to the target nucleotide repeats preferentially over other nucleotide repeats or nucleotide sequences.
  • the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CGG.
  • the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CCG.
  • the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CCTG.
  • the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of TGGAA. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of GGGGCC. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CAG. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CTG.
  • the transcription modulation molecules described herein become localized around regions having multiple repeats of GAA.
  • the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CGG.
  • the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CCG.
  • the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CCTG.
  • the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of TGGAA. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of GGGGCC. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CTG. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CAG.
  • the first terminus is localized to a sequence having multiple repeats of GAA and binds to the target nucleotide repeats preferentially over other nucleotide repeats.
  • the sequence has at least 2, 3, 4, 5, 8, 10, 12, 15, 20, 25, 30, 40, 50, 100, 200, 300, 400, or 500 repeats of GAA.
  • the sequence comprises at least 1000 nucleotide repeats of GAA.
  • the sequence comprises at least 500 nucleotide repeats of GAA.
  • the sequence comprises at least 200 nucleotide repeats of GAA.
  • the sequence comprises at least 100 nucleotide repeats of GAA.
  • the sequence comprises at least 50 nucleotide repeats of GAA.
  • the sequence comprises at least 20 nucleotide repeats of GAA.
  • the compounds of the present disclosure can bind to the repeated GAA of fxn than to GAA elsewhere in the subject's DNA.
  • the polyamide composed of a pre-selected combination of subunits can selectively bind to the DNA in the minor groove.
  • antiparallel side-by-side pairings of two aromatic amino acids bind to DNA sequences, with a polyamide ring packed specifically against each DNA base.
  • N-Methylpyrrole (Py) favors T, A, and C bases, excluding G;
  • N-methylimidazole (Im) is a G-reader; and 3-hydroxyl-N-methylpyrrol (Hp) is specific for thymine base.
  • the nucleotide base pairs can be recognized using different pairings of the amino acid subunits using the paring principle shown in Table 1A and 1B below.
  • an Im/Py pairing reads GC by symmetry
  • a Py/Im pairing reads C ⁇ G
  • an Hp/Py pairing can distinguish T ⁇ A from A ⁇ T, G ⁇ C, and C ⁇ G
  • a Py/Py pairing nonspecifically discriminates both A ⁇ T and T.A from G ⁇ C and C ⁇ G.
  • the first terminus comprises Im corresponding to the nucleotide G; Py or beta corresponding to the nucleotide A; Py corresponding to the nucleotide A, wherein Im is N-alkyl imidazole, Py is N-alkyl pyrrole, and beta is ⁇ -alanine.
  • the first terminus comprises Im/Py to correspond to the nucleotide pair G/C, Py/beta or Py/Py to correspond to the nucleotide pair A/T, and wherein Im is N-alkyl imidazole (e.g, N-methyl imidazole), Py is N-alkyl pyrrole (e.g., N-methyl pyrrole), and beta is ⁇ -alanine.
  • Im is N-alkyl imidazole (e.g, N-methyl imidazole)
  • Py is N-alkyl pyrrole (e.g., N-methyl pyrrole)
  • beta is ⁇ -alanine.
  • HpBi, ImBi, and PyBi corresponds to Hp-Py, Im-Py, and Py-Py respectively.
  • Table 1B Base paring for hairpin polyamide G ⁇ C C ⁇ G T ⁇ A A ⁇ T Im/ ⁇ + - - - ⁇ /Im - + - - Py/ ⁇ - - + + ⁇ /Py - - + + ⁇ / ⁇ - - + + Py/Py - - + + Im/Im - - - - Im/Py + - - - - Py/Im - + - - Th/Py - - + - Py/Th - - - + Th/Im + - - - Im/Th - + - - ⁇ /Th - - + - Th/ ⁇ - - - + Hp/Py, - - + - Py/Hp, - - - + Hp/Im +
  • the monomer subunits of the polyamide can be strung together based on the paring principles shown in Table 1A and Table 1B.
  • the monomer subunits of the polyamide can be strung together based on the paring principles shown in Table 1C and Table 1D.
  • Table 1C shows an example of the monomer subunits that can bind to the specific nucleotide.
  • the first terminus can include a polyamide described having several monomer subunits stung together, with a monomer subunit selected from each row.
  • the polyamide can include Im- ⁇ -Py that binds to GAA, with Im selected from the first G column, ⁇ from the A column, and Py from the second A column.
  • the polyamide can be any combinations that bind to the subunits of GAA, with a subunit selected from each column in Table 1C, wherein the subunits are strung together following the GAA order.
  • the polyamide can also include a partial or multiple sets of the five subunits, such as 1.5, 2, 2.5, 3, 3.5, or 4 sets of the three subunits.
  • the polyamide can include 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, and 16 monomer subunits. The multiple sets can be joined together by W.
  • the polyamide can also include 1-4 additional subunits that can link multiple sets of the five subunits.
  • the polyamide can include monomer subunits that bind to 2, 3, 4, or 5 nucleotides of GAA.
  • the polyamide can bind to GA, AA, GAA, AAG, AGA, GAAG, AAGA, GAAGA or GAAGAA.
  • the polyamide can include monomer subunits that bind to 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides of GAA repeats.
  • the nucleotides can be joined by W.
  • the monomer subunit when positioned as a terminal unit, does not have an amine or a carboxylic acid group at the terminal.
  • the amine or carboxylic acid group in the terminal is replaced by a hydrogen.
  • Py when used as a terminal unit, is understood to have the structure of (e.g, ); and Im, when positioned as a terminal unit, is understood to have the structure of (e.g, ).
  • Py and Im when positioned as a terminal unit, Py and Im can be respectively replaced by PyT (e.g., ) and ImT (e.g., ).
  • the linear polyamide can have nonlimiting examples including but not limited ⁇ -Py-Im, Im-Py- ⁇ -Im-Py- ⁇ -Im-Py, Im-Py- ⁇ -Im-Py-Py-lm- ⁇ , Im-Py-Py-Im-Py- ⁇ -Im- ⁇ , and any combinations thereof.
  • Table 1C Examples of monomer subunits in a linear polyamide that binds to GAA.
  • Nucleotide G A Subunit that selectively binds to nucleotide Im or ImT Py Py ilm or iImT Th Th PEG Pz Pz CTh Tp Tp Nt PEG PEG iPTA ⁇ ⁇ Ip iPP iPP CTh Da Da Dp Dp Dab Dab gAH gAH
  • the DNA-binding moiety can also include a hairpin polyamide having subunits that are strung together based on the pairing principle shown in Table 1B.
  • Table 1D shows some examples of the monomer subunit pairs that selectively bind to the nucleotide pair.
  • the hairpin polyamide can include 2n monomer subunits (n is an integer in the range of 2-8), and the polyamide also includes a W in the center of the 2n monomer subunits.
  • W can be -(CH 2 ) a -NR 1 -(CH 2 ) b -, -(CH 2 ) a -, -(CH 2 ) a -O-(CH 2 ) b -, -(CH 2 ) a -CH(NHR 1 )-, - (CH 2 ) -CH(NHR 1 )-, -(CR 2 R 3 ) a -or -(CH 2 ) a -CH(NR 1 3 ) + -(CH 2 ) b -, wherein each a is independently an integer between 2 and 4; R 1 is H, an optionally substituted C 1-6 alkyl, an optionally substituted C 3-10 cycloalkyl, an optionally substituted C 6-10 aryl, an optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; each R 2 and R 3 are independently H, halogen, OH, NHAc
  • W is -(CH 2 )-CH(NH 3 ) + -(CH 2 )- or -(CH 2 )-CH 2 CH(NH 3 ) + -.
  • R 1 is H.
  • R 1 is C 1-6 alkyl optionally substituted by 1-3 substituents selected from -C(O)-phenyl.
  • W is -(CR 2 R 3 )-(CH 2 )a- or -(CH 2 ) a -(CR 2 R 3 )-(CH 2 ) b -, wherein each a is independently 1-3, b is 0-3, and each R 2 and R 3 are independently H, halogen, OH, NHAc, or C 1-4 alky.
  • W can be an aliphatic amino acid residue shown in Table 4 such as gAB.
  • the polyamide When n is 2, the polyamide includes 4 monomer subunits, and the polyamide also includes a W joining the first set of two subunits with the second set of two subunits, Q1-Q2-W-Q3-Q4, and Q1/Q4 correspond to a first nucleotide pair on the DNA double strand, Q2/Q3 correspond to a second nucleotide pair, and the first and the second nucleotide pair is a part of the GAA repeat.
  • the polyamide includes 6 monomer subunits, and the polyamide also includes a W joining the first set of three subunits with the second set of three subunits, Q1-Q2-Q3-W-Q4-Q5-Q6, and Q1/Q6 correspond to a first nucleotide pair on the DNA double strand, Q2/Q5 correspond to a second nucleotide pair, Q3/Q4 correspond to a third nucleotide pair, and the first and the second nucleotide pair is a part of the A repeat.
  • the polyamide When n is 4, the polyamide includes 8 monomer subunits, and the polyamide also includes a W joining the first set of four subunits with the second set of four subunits, Q1-Q2-Q3-Q4-W-Q5-Q6-Q7-Q8, and Q1/Q8 correspond to a first nucleotide pair on the DNA double strand, Q2/Q7 correspond to a second nucleotide pair, Q3/Q6 correspond to a third nucleotide pair, and Q4/Q5 correspond to a fourth nucleotide pair on the DNA double strand.
  • the polyamide When n is 5, the polyamide includes 10 monomer subunits, and the polyamide also includes a W joining a first set of five subunits with a second set of five subunits, Q1-Q2-Q3-Q4-Q5-W-Q6-Q7-Q8-Q9-Q10, and Q1/Q10, Q2/Q9, Q3/Q8, Q4/Q7, Q5/Q6 respectively correspond to the first to the fifth nucleotide pair on the DNA double strand.
  • the polyamide When n is 6, the polyamide includes 12 monomer subunits, and the polyamide also includes a W joining a first set of six subunits with a second set of six subunits, Q1-Q2-Q3-Q4-Q5-Q6-W-Q7-Q8-Q9-Q10-Q11-Q12, and Q1/Q12, Q2/Q11, Q3/Q10, Q4/Q9, Q5/Q8, Q6/Q7 respectively correspond to the first to the six nucleotide pair on the DNA double strand.
  • the polyamide When n is 8, the polyamide includes 16 monomer subunits, and the polyamide also includes a W joining a first set of eight subunits with a second set of eight subunits, Q1-Q2-Q3-Q4-Q5-Q6-Q7-Q8-W-Q9-Q10-Q11-Q12-Q13-Q14-Q15-Q16, and Q1/Q16, Q2/Q15, Q3/Q14, Q4/Q13, Q5/Q12, Q6/Q11, Q7/Q10, and Q8/Q9 respectively correspond to the first to the eight nucleotide pair on the DNA double strand.
  • the number of monomer subunits on each side of W can be different, and one side of the hairpin can partial pair with the other side of the hairpin to bind the nucleotide pairs on a double strand DNA based on the binding principle in Table 1B and 1D, while the rest of the unpaired monomer subunit(s) can bind to the nucleotide based on the binding principle in Table 1A and 1C but does not pair with the mononer subunit on the other side.
  • the hairpin polyamide can have one or more overhanging monomer subunit that binds to the nucleotide but does not pair with the monomer subunit on the antiparrallel strand
  • the hairpin structure can include 5 monomer subunits on one side of W and 4 monomer subunits on the other side of W, Q1-Q2-Q3-Q4-Q5-W-Q6-Q7-Q8-Q9, and Q2/Q9, Q3/Q8, Q4/Q7, Q5/Q6 respectively correspond to the first to the fourth nucleotide pair on the DNA double strand, and Q1 binds to a single nucleotide but does not pair with a monomer subunit on the other strand to bind with a nucleotide pair.
  • W can be an aliphatic amino acid residue such as gAB or other appropriate spacers as shown in Table 4. In some instances, when W is gAB, it favors binding to T.
  • the subunits can be strung together to bind at least two, three, four, five, six, seven, eight, nine, or ten nucleotides in one or more GAA repeat (e.g., GAAGAAGAAGAA).
  • the polyamide can bind to the GAA repeat by binding to a partial copy, a full copy, or a multiple repeats of GAA such as GA, AA, GAA, AAG, AGA, GAAG, AAGA, GAAGA or GAAGAA.
  • the polyamide can include Im-Py- ⁇ -W-Py- ⁇ -Py that binds to GAA and its complementary nucleotides on a double strand DNA, in which the Im/Py pair binds to the G ⁇ C, the Py/ ⁇ pair binds to A ⁇ T, and the ⁇ /Py pair binds to G.A.
  • Im-Py- ⁇ -Im-W- ⁇ -Py- ⁇ -Py that binds to GAAG and its complementary nucleotides on a double strand DNA, in which the Im/Py pair binds to the G ⁇ C, the Py/ ⁇ pair binds to A ⁇ T, the ⁇ /Py pair binds to G ⁇ A, and the Im/ ⁇ pair binds to the G ⁇ C,.
  • W can be an aliphatic amino acid residue such as gAB or other appropriate spacers as shown in Table 4.
  • Im-Py- ⁇ -Im-gAB-Im-Py binds to with a part of the complementary nucletides (ACG) on the double strand DNA, in wihch Im binds to G, Py binds to A, ⁇ /Py binds to the A ⁇ T, Im/Im binds to G ⁇ C.
  • ACG complementary nucletides
  • polyamide examples include but are not limited to Im-Py-Py-Im-gAB-Py-Im-Im-Py; Im-Py-Py-Im-gAB-Py-Im-Im-PyT; Im-Py-Py-Im-gAB-Py-Im-Im- ⁇ ; Im-Py-Py-Im-gAB-Py-Im-Im- ⁇ -G; Im- ⁇ -Py-Im-gAB-Py-Im-Im- ⁇ ; Im- ⁇ -Py-Im-gAB-Py-Im-Im-Im- ⁇ -G; Im- ⁇ -Py-Im-gAB-Py-Im-Im-Im-Py; Im- ⁇ -Py-Im-gAB-Py-Im-Im-Im-PyT; Py-Py-Im- ⁇ -gAB-Im-Py-Im-Im; Py-Py-
  • the hairpin polyamide has a structure of Im-Py- ⁇ -Im-gAB-Im-Py; Im-Py- ⁇ -Im-gAB-Im-Py- ⁇ -Im; Py- ⁇ -Im-gAB-Im-Py- ⁇ -Im; or ⁇ -Im-gAB-Im-Py- ⁇ -Im.
  • Table 1D Examples of monomer pairs in a hairpin or H-pin polyamide that binds to GAA.
  • Recognition of a nucleotide repeat or DNA sequence by two antiparallel polyamide strands depends on a code of side-by-side aromatic amino acid pairs in the minor groove, usually oriented N to C with respect to the 5' to 3' direction of the DNA helix. Enhanced affinity and specificity of polyamide nucleotide binding is accomplished by covalently linking the antiparallel strands.
  • the "hairpin motif” connects the N and C termini of the two strands with a W (e.g., gamma-aminobutyric acid unit (gamma-turn)) to form a folded linear chain.
  • W e.g., gamma-aminobutyric acid unit (gamma-turn)
  • the "H-pin motif” connects the antiparallel strands across a central or near central ring/ring pairs by a short, flexible bridge.
  • the DNA-binding moiety can also include a H-pin polyamide having subunits that are strung together based on the pairing principles shown in Table 1A and/or Table 1B.
  • Table 1C shows some examples of the monomer subunit that selectively binds to the nucleotide
  • Table 1D shows some examples of the monomer subunit pairs that selectively bind to the nucleotide pair.
  • the h-pin polyamide can include 2 strands and each strand can have a number of monomer subunits (each strand can include 2-8 monomer subunits), and the polyamide also includes a bridge L 1 to connect the two strands in the center or near the center of each strand.
  • At least one or two of the monomer subunits on each strand are paired with the corresponding monomer subunits on the other stand following the paring principle in Table 1D to favor binding of either GC or C ⁇ G, A ⁇ T, or T ⁇ A pair, and these monomer subunit pairs are often positioned in the center, close to center region, at or close to the bridge that connects the two strands.
  • the H-pin polyamide can have all of the monomer subunits be paired with the corresponding monomer subunits on the antiparallel strand based on the paring principle in Table 1B and 1D to bind to the nucleotide pairs on the double strand DNA.
  • the H-pin polyamide can have a part of the monomer subunits (2, 3, 4, 5, or 6) be paired with the corresponding monomer subunits on the antiparallel strand based on the binding principle in Table 1B and 1D to bind to the nucleotide pairs on the double strand DNA, while the rest of the monomer subunit binds to the nucleotide based on the binding principle in Table 1A and 1C but does not pair with the mononer subunit on the antiparallel strand.
  • the h-pin polyamide can have one or more overhanging monomer subunit that binds to the nucleotide but does not pair with the nomoner subunit on the antiparrallel strand.
  • Another polyamide structure that derives from the h-pin structure is to connect the two antiparallel strands at the end through a bridge, while only the two mononer subunits that are connected by the bridge form a pair that bind to the nucleotide pair G ⁇ C or C.G based on the binding principle in Table 1B/1D, but the rest of the monomer subunits on the strand form an overhang, bind to the nucleotide based on the binding principle in Table 1A and/or 1C and do not pair with the monomer subunit on the other strand.
  • the bridge can be is a bivalent or trivalent group selected from a C 1-10 alkylene, -NH-C 0-6 alkylene-C(O)-, -N(CH 3 )-C 0-6 alkylene, and -(CH 2 ) a -NR 1 -(CH 2 ) b -, - (CH 2 ) a -, -(CH 2 ) a -O-(CH 2 ) b -, -(CH 2 ) a -CH(NHR 1 )-, -(CH 2 ) a -CH(NHR 1 )-, -(CR 2 R 3 ) a - or -(CH 2 ) a -CH(NR 1 3 ) + -(CH 2 ) b -, wherein m is an integer in the range of 0 to 10; n is an integer in the range of 0 to 10; each a is independently an integer between 2 and 4; R 1 is H, an optional
  • W is -(CH 2 )-CH(NH 3 ) + -(CH 2 )- or -(CH 2 )-CH 2 CH(NH 3 ) + -.
  • R 1 is H.
  • R 1 is C 1-6 alkyl optionally substituted by 1-3 substituents selected from -C(O)-phenyl.
  • L 1 is -(CR 2 R 3 )-(CH 2 ) a - or -(CH 2 ) a -(CR 2 R 3 )-(CH 2 ) b -, wherein each a is independently 1-3, b is 0-3, and each R 2 and R 3 are independently H, halogen, OH, NHAc, or C 1-4 alky.
  • L 1 can be a C 2-9 alkylene or (PEG) 2-8 .
  • the polyamide includes 6 monomer subunits, and the polyamide also includes a bridge L 1 joining the first set of three subunits with the second set of three subunits, and Q1-Q2-Q3 can be joined to Q4-Q5-Q6 through L 1 at the center Q2 and Q5, and Q1/Q4 correspond to a first nucleotide pair on the DNA double strand, Q2/Q5 correspond to a second nucleotide pair, Q3/Q6 correspond to a third nucleotide pair.
  • the polyamide When n is 4, the polyamide includes 8 monomer subunits, and the polyamide also includes a bridge L 1 joining the first set of four subunits with the second set of four subunits, Q1-Q2-Q3-Q4 can be joined to Q5-Q6-Q7-Q8 through L 1 at Q2 and Q6 Q2 and Q7, Q3 and Q6, or Q3 and Q7 positions; Q1/Q5 may correspond to a nucleotide pair on the DNA double strand, and Q3/Q8 may correspond to another nucleotide pair; or Q1 and Q8 form overhangs on each strand, or Q and Q5 form overhangs on each strand.
  • the polyamide When n is 5, the polyamide includes 10 monomer subunits, and the polyamide also includes a bridge L 1 joining a first set of five subunits with a second set of five subunits, and Q1-Q2-Q3-Q4-Q5 can be joined to Q6-Q7-Q8-Q9-Q10 through a bridge L 1 at non-terminal positions (any position except for Q1, Q5, Q6 and Q10); if the two strands are linked at Q3 and Q8 by the bridge, Q1/Q6, Q2/Q7, Q3/Q8, Q4/Q9, and Q5/Q10 can be paired to bind to the nucleotide pairs; if the two strands are linked at Q2 and Q9 by the bridge, then Q1/Q8, Q3/Q10 can be paired to bind to the nucleotide pairs, Q4 and Q5 form an overhang on one strand and Q6 and Q7 form an overhang on the other strand.
  • the monomer subunit at the central or near the central (n/2, (n ⁇ 1)/2) on one strand is paired with the corresponding one on the other strand to bind to the nucleotide pairs on the double stranded DNA.
  • the monomer subunit at the central or near the central (n/2, ( n ⁇ 1)/2) on one strand is connected with the corresponding one on the other strand through a bridge L 1 .
  • the polyamide When n is 4, the polyamide includes 8 monomer subunits, and the polyamide also includes a bridge L 1 joining the first set of four subunits with the second set of four subunits, Q1-Q2-Q3-Q4 can be joined to Q5-Q6-Q7-Q8 at the end Q4 and Q5 through L 1; while Q4/Q5 can be paired to bind to the nucleotide pairs, Q1-Q2-Q3 form an overhang on one strand and Q6-Q7-Q8 form an overhang on the other strand.
  • polyamide examples include but are not limited to Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py, Im-Py-Py-Im (Linked in the middle - position 3 py and Py) to Im-Py- ⁇ -Py-Py, Im-Py- ⁇ -Im (linked to the bolded position) Im-Py ; Im- Py- ⁇ -Im (linked in the middle, either position 2 or 3) Im- Py-b -Im; Py- ⁇ - Im (linked to the middle position bolded) Im -Py- ⁇ -Im; or ⁇ - Im (linked at bolded position) Im -Py- ⁇ -Im.
  • the regulatory molecule is chosen from a nucleosome remodeling factor (NURF), a bromodomain PHD finger transcription factor (BPTF), a ten-eleven translocation enzyme (TET), methylcytosine dioxygenase (TET1), a DNA demethylase, a helicase, an acetyltransferase, and a histone deacetylase ("HDAC").
  • NURF nucleosome remodeling factor
  • BPTF bromodomain PHD finger transcription factor
  • TET ten-eleven translocation enzyme
  • TET1 methylcytosine dioxygenase
  • DNA demethylase a helicase
  • acetyltransferase a histone deacetylase
  • the binding affinity between the regulatory protein and the second terminus can be adjusted based on the composition of the molecule or type of protein.
  • the second terminus binds the regulatory molecule with an affinity of less than about 600 nM, about 500 nM, about 400 nM, about 300 nM, about 250 nM, about 200 nM, about 150 nM, about 100 nM, or about 50nM.
  • the second terminus binds the regulatory molecule with an affinity of less than about 300 nM.
  • the second terminus binds the regulatory molecule with an affinity of less than about 200 nM.
  • the polyamide is capable of binding the DNA with an affinity of greater than about 200 nM, about 150 nM, about 100 nM, about 50 nM, about 10 nM, or about 1 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity in the range of about 1-600 nM, 10-500 nM, 20-500 nM, 50-400 nM, 100-300 nM, or 50-200 nM.
  • the second terminus comprises one or more optionally substituted C 6-10 aryl, optionally substituted C 4-10 carbocyclic, optionally substituted 4 to 10 membered heterocyclic, or optionally substituted 5 to 10 membered heteroaryl.
  • the protein-binding moiety binds to the regulatory molecule that is selected from the group consisting of a CREB binding protein (CBP), a P300, an O-linked ⁇ -N-acetylglucosamine-transferase- (OGT-), a P300-CBP-associated-factor- (PCAF-), histone methyltransferase, histone demethylase, chromodomain, a cyclin-dependent-kinase-9- (CDK9-), a nucleosome-remodeling-factor-(NURF-), a bromodomain-PHD-finger-transcription-factor- (BPTF-), a ten-eleven-translocation-enzyme-(TET-), a methylcytosine-dioxygenase- (TET1-), histone acetyltransferase (HAT), a histone deacetalyse (HDAC), , a host-
  • CBP
  • the second terminus comprises a moiety that binds to an O-linked ⁇ -N-acetylglucosamine-transferase (OGT), or CREB binding protein (CBP).
  • the protein binding moiety is a residue of a compound that binds to an O-linked ⁇ -N-acetylglucosamine-transferase(OGT), or CREB binding protein (CBP).
  • the second terminus does not comprises JQ1, iBET762, OTX015, RVX208, or AU1. In some embodiments, the second terminus does not comprises JQ1. In some embodiments, the second terminus does not comprises a moiety that binds to a bromodomain protein.
  • the second terminus comprises a diazine or diazepine ring, wherein the diazine or diazepine ring is fused with a C 6-10 aryl or a 5-10 membered heteroaryl ring comprising one or more heteroatom selected from S, N and O.
  • the second terminus comprises an optionally substituted bicyclic or tricyclic structure.
  • the optionally substituted bicyclic or tricyclic structure comprises a diazepine ring fused with a thiophene ring.
  • the second terminus does not comprise an optionally substituted bicyclic structure, wherein the bicyclic structure comprises a diazepine ring fused with a thiophene ring.
  • the second terminus does not comprise an optionally substituted tricyclic structure, wherein the tricyclic structure is a diazephine ring that is fused with a thiophene and a triazole.
  • the second terminus does not comprise an optionally substituted diazine ring.
  • the second terminus does not comprise a structure of Formula (C-11): wherein:
  • X 1p is N.
  • a 1p is an aryl or heteroaryl substituted with one or more substituents.
  • a 1p is an aryl or heteroaryl substituted with one or more substituents selected from halogen, C 1-6 alkyl, hydroxyl, C 1-6 alkoxy, and C 1-6 haloalkyl.
  • B 1p is an optionally substituted aryl or heteroaryl substituted with one or more substituents selected from halogen, C 1-6 alkyl, hydroxyl, C 1-6 alkoxy, and C 1-6 haloalkyl.
  • a 1p is an optionally substituted thiophene or phenyl. In some embodiments, A 1p is a thiophene or phenyl, each substituted with one or more substituents selected from halogen, C 1-6 alkyl, hydroxyl, C 1-6 alkoxy, and C 1-6 haloalkyl. In some embodiments, B 1p is an optionally substituted triazole. In some embodiments, B 1p is a triazole substituted with one or more substituents selected from halogen, C 1-6 alkyl, hydroxyl, C 1-6 alkoxy, and C 1-6 haloalkyl.
  • the protein binding moiety is not
  • the protein binding moiety is not
  • the protein binding moiety does not have the structure of Formula (C-12): wherein:
  • the protein binding moiety can include a residue of a compound that binds to a regulatory protein.
  • the protein binding moiety can be a residue of a compound shown in Table 2.
  • Exemplary residues include, but are not limited to, amides, carboxylic acid esters, thioesters, primary amines, and secondary amines of any of the compounds shown in Table 2.
  • the second terminus does not comprises JQ1, JQ-1, OTX015, RVX208 acid, or RVX208 hydroxyl.
  • the protein binding moiety is a residue of a compound having a structure of Formula (C-1): wherein:
  • the protein binding moiety is a residue of a compound having a structure of Formula (C-2): wherein R 5e is independently selected from the group consisting of H, COOC 1-10 alkyl, NHC(O)-optionally substituted -C 1-12 alkyl, optionally substituted -C 2-10 alkenyl, optionally substituted -C 2-10 alkynyl, optionally substituted -C 1-12 alkoxyl, optionally substituted -C 1-12 haloalkyl, optionally substituted C 6-10 aryl, optionally substituted C 3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkylsubstituted -C 2-10 alkenyl, optionally substituted -C 2-10 alkynyl, optionally substituted -C 1-12 alkoxyl, optionally substituted -C 1-12 haloalkyl, optionally substituted C 6-10
  • a a is selected from an optionally substituted C 6-10 aryl, optionally substituted C 3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5-to 10-membered heterocycloalkyl. In certain embodiments, A a is an optionally substituted C 6-10 aryl.
  • the protein binding moiety is a residue of a compound having a structure of Formula (C-3): wherein:
  • each R 1h and R 5h are independently hydrogen, halogen, or C 1-6 alkyl.
  • each R 2h and R 3h are independently H, OH, -NO 2 , halogen, C 1-4 haloalkyl, amine, COOH, COOC 1-10 alkyl, -NHC(O)-optionally substituted -C 1-12 alkyl, -NHC(O)(CH 2 ) 1-4 NR f R g , - NHC(O)(CH 2 ) 0-4 CHR'(NR'R"), -NHC(O)(CH 2 ) 0-4 CHR f R g , -NHC(O)(CH 2 ) 0-4 -C 3-7 cycloalkyl, - NHC(O)(CH 2 ) 0-4 -5- to 10-membered heterocycloalkyl, NHC(O)(CH 2 ) 0-4 C 6-10 aryl, -NH
  • R 2e is selected from the group consisting of H, OH, -NO 2 , halogen, amine, COOH, COOC 1-10 alkyl, NHC(O)-optionally substituted -C 1-12 alkyl, NHC(O)(CH 2 ) 1-4 NR f R g , - NHC(O)(CH 2 ) 0-4 CHR f (NR f R g ), -NHC(O)(CH 2 ) 0-4 CHR f R g , -NHC(O)(CH 2 ) 0-4 -C 3-7 cycloalkyl, - NHC(O)(CH 2 ) 0-4 -5- to 10-membered heterocycloalkyl, NHC(O)(CH 2 ) 0-4 C 6-10 aryl, -NHC(O)(CH 2 ) 0-4 -5- to 10-membered heteroaryl, -(CH 2 ) 1-4 -C 3-7
  • R 2e is an phenyl or pyridinyl optionally substituted with 1-3 substituents, wherein the substituent is independently selected from the group consisting of OH, -NO 2 , halogen, amine, COOH, COOC 1-10 alkyl, NHC(O) -C 1-12 alkyl, -NHC(O)(CH 2 ) 1-4 NR f R g , -NHC(O)(CH 2 ) 0-4 CHR f (NR f R g ), - NHC(O)(CH 2 ) 0-4 CHR f R g , -NHC(O)(CH 2 ) 0-4 -C 3-7 cycloalkyl, -NHC(O)(CH 2 ) 0-4 -5- to 10-membered heterocycloalkyl, NHC(O)(CH 2 ) 0-4 C 6-10 aryl, -NHC(O)(CH 2 ) 0-4 -5- to 10-
  • a a is a C 6-10 aryl substituted with 1-4 substituents, and each substituent is independently selected from halogen, OH, NO 2 , an optionally substituted -C 1-12 alkyl, optionally substituted -C 2-10 alkenyl, optionally substituted -C 2-10 alkynyl, optionally substituted -C 1-12 alkoxyl, optionally substituted -C 1-12 haloalkyl, optionally substituted C 6-10 aryl, optionally substituted C 3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl.
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-4): wherein:
  • R 2j is -NHC(CH 3 ) 3 , or a 4- to 10-membered heterocycloalkyl substituted with C 1-12 alkyl.
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-5): wherein:
  • R 2j is a 4- to 10-membered heterocycloalkyl substituted by a 4- to 10-membered heterocycloalkyl.
  • R 6j is -C(O)R 3j
  • R 3j is a 4- to 10-membered heterocycloalkyl substituted by a 4- to 10-membered heterocycloalkyl.
  • each R 5j is independently H, -C(O)R 3j , -COOH, -C(O)NHC 1-6 alkyl, -NH-C 6-10 aryl, or optionally substituted C 6-10 aryl
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-6): wherein:
  • R 7j is an optionally substituted cyclic secondary or tertiary amine. In certain embodiments, R 7j is a tetrahydroisoquinoline optionally substituted with C 1-4 alkyl.
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-7): wherein:
  • a 1a is an aryl substituted with one or more halogen, C 1-6 alkyl, hydroxyl, C 1-6 alkoxy, or C 1-6 haloalkyl.
  • X 2 is NH.
  • a 2a is a heterocyclic group.
  • a 2a is a pyrrolidine.
  • a 2a is an optionally substituted phenyl.
  • a 2a is a phenyl optionally substituted with one or more halogen, C 1-6 alkyl, hydroxyl, C 1-6 alkoxy, or C 1-6 haloalkyl.
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-8): wherein R 1k is H or C 1-25 alkyl and R 2k is OH or -OC 1-12 alkyl.
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-9):
  • the protein binding moiety is a residue of a compound having the structure of Formula (C-10):
  • the regulatory molecule is not a bromodomain-containing protein chosen from BRD2, BRD3, BRD4, and BRDT.
  • the regulatory molecule is BRD4.
  • the recruiting moiety is a BRD4 activator.
  • the BRD4 activator is chosen from JQ-1, OTX015, RVX208 acid, and RVX208 hydroxyl.
  • the regulatory molecule is BPTF.
  • the recruiting moiety is a BPTF activator.
  • the BPTF activator is AU1.
  • the regulatory molecule is histone acetyltransferase ("HAT").
  • the recruiting moiety is a HAT activator.
  • the HAT activator is a oxopiperazine helix mimetic OHM.
  • the HAT activator is selected from OHM1, OHM2, OHM3, and OHM4 ( BB Lao et al., PNAS USA 2014, 111(21), 7531-7536 ).
  • the HAT activator is OHM4.
  • the regulatory molecule is histone deacetylase ("HDAC").
  • HDAC histone deacetylase
  • the recruiting moiety is an HDAC activator.
  • the HDAC activator is chosen from SAHA and 109 ( Soragni E Front. Neurol. 2015, 6, 44 , and references therein).
  • the regulatory molecule is histone deacetylase ("HDAC").
  • HDAC histone deacetylase
  • the recruiting moiety is an HDAC inhibitor.
  • the HDAC inhibitor is an inositol phosphate.
  • the regulatory molecules is O-linked ⁇ -N-acetylglucosamine transferase ("OGT").
  • the recruiting moiety is an OGT activator.
  • the OGT activator is chosen from ST045849, ST078925, and ST060266 ( Itkonen HM, "Inhibition of O-GlcNAc transferase activity reprograms prostate cancer cell metabolism", Oncotarget 2016, 7(11), 12464-12476 ).
  • the regulatory molecule is chosen from host cell factor 1 ("HCF1") and octamer binding transcription factor (“OCT1").
  • the recruiting moiety is chosen from an HCF1 activator and an OCT1 activator.
  • the recruiting moiety is chosen from VP16 and VP64.
  • the regulatory molecule is chosen from CBP and P300.
  • the recruiting moiety is chosen from a CBP activator and a P300 activator. In certain embodiments, the recruiting moiety is CTPB.
  • the regulatory molecule is P300/CBP-associated factor ("PCAF").
  • the recruiting moiety is a PCAF activator.
  • the PCAF activator is embelin.
  • the regulatory molecule modulates the rearrangement of histones.
  • the regulatory molecule modulates the glycosylation, phosphorylation, alkylation, or acylation of histones.
  • the regulatory molecule is a transcription factor.
  • the regulatory molecule is an RNA polymerase.
  • the regulatory molecule is a moiety that regulates the activity of RNA polymerase.
  • the regulatory molecule interacts with TATA binding protein.
  • the regulatory molecule interacts with transcription factor II D.
  • the regulatory molecule comprises a CDK9 subunit.
  • the regulatory molecule is P-TEFb.
  • X binds to the regulatory molecule but does not inhibit the activity of the regulatory molecule. In certain embodiments, X binds to the regulatory molecule and inhibits the activity of the regulatory molecule. In certain embodiments, X binds to the regulatory molecule and increases the activity of the regulatory molecule.
  • X binds to the active site of the regulatory molecule. In certain embodiments, X binds to a regulatory site of the regulatory molecule.
  • the recruiting moiety is chosen from a CDK-9 inhibitor, a cyclin T1 inhibitor, and a PRC2 inhibitor.
  • the recruiting moiety is a CDK-9 inhibitor.
  • the CDK-9 inhibitor is chosen from flavopiridol, CR8, indirubin-3'-monoxime, a 5-fluoro-N2,N4-diphenylpyrimidine-2,4-diamine, a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine, TG02, CDKI-73, a 2,4,5-trisubstited pyrimidine derivatives, LCD000067, Wogonin, BAY-1000394 (Roniciclib), AZD5438, and DRB ( F Morales et al. "Overview of CDK9 as a target in cancer research", Cell Cycle 2016, 15(4), 519-527 , and references therein).
  • the regulatory molecule is a histone demethylase.
  • the histone demethylase is a lysine demethylase.
  • the lysine demethylase is KDM5B.
  • the recruiting moiety is a KDM5B inhibitor.
  • the KDM5B inhibitor is AS-8351 ( N. Cao, Y. Huang, J. Zheng,et al., "Conversion of human fibroblasts into functional cardiomyocytes by small molecules", Science 2016, 352(6290),1216-1220 , and references therein.)
  • the regulatory molecule is the complex between the histone lysine methyltransferases ("HKMT”) GLP and G9A ("GLP/G9A").
  • the recruiting moiety is a GLP/G9A inhibitor.
  • the GLP/G9A inhibitor is BIX-01294 ( Chang Y, "Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294", Nature Struct. Mol. Biol. 2009, 16, 312-317 , and references therein).
  • the regulatory molecule is a DNA methyltransferase ("DNMT").
  • the regulatory moiety is DNMT1.
  • the recruiting moiety is a DNMT1 inhibitor.
  • the DNMT1 inhibitor is chosen from RG108 and the RG108 analogues 1149, T1, and G6. ( B Zhu et al. BioorgMed Chem 2015, 23(12), 2917-2927 and references therein).
  • the recruiting moiety is a PRC1 inhibitor.
  • the PRC1 inhibitor is chosen from UNC4991, UNC3866, and UNC3567 ( JI Stuckey et al. Nature Chem Biol 2016, 12(3), 180-187 and references therein; KD Bamash et al. ACS Chem. Biol. 2016, 11(9), 2475-2483 , and references therein).
  • the recruiting moiety is a PRC2 inhibitor.
  • the PRC2 inhibitor is chosen from A-395, MS37452, MAK683, DZNep, EPZ005687, EI1, GSK126, and UNC1999 ( Konze KD ACS Chem Biol 2013, 8(6), 1324-1334 , and references therein).
  • the recruiting moiety is rohitukine or a derivative of rohitukine.
  • the recruiting moiety is DB08045 or a derivative of DB08045.
  • the recruiting moiety is A-395 or a derivative of A-395.
  • the regulatory molecule is chosen from a bromodomain-containing protein, a nucleosome remodeling factor (NURF), a bromodomain PHD finger transcription factor (BPTF), a ten-eleven translocation enzyme (TET), methylcytosine dioxygenase (TET1), a DNA demethylase, a helicase, an acetyltransferase, and a histone deacetylase ("HDAC").
  • NURF nucleosome remodeling factor
  • BPTF bromodomain PHD finger transcription factor
  • TET ten-eleven translocation enzyme
  • TET1 methylcytosine dioxygenase
  • DNA demethylase a helicase
  • HDAC histone deacetylase
  • the regulatory molecule is a bromodomain-containing protein chosen from BRD2, BRD3, BRD4, and BRDT.
  • the regulatory molecule is BRD4.
  • the recruiting moiety is a BRD4 activator.
  • the BRD4 activator is chosen from JQ-1, OTX015, RVX208 acid, and RVX208 hydroxyl.
  • the regulatory molecule is BPTF.
  • the recruiting moiety is a BPTF activator.
  • the BPTF activator is AU1.
  • the regulatory molecule is histone acetyltransferase ("HAT").
  • the recruiting moiety is a HAT activator.
  • the HAT activator is a oxopiperazine helix mimetic OHM.
  • the HAT activator is selected from OHM1, OHM2, OHM3, and OHM4 ( BB Lao et al., PNAS USA 2014, 111(21), 7531-7536 ).
  • the HAT activator is OHM4.
  • the regulatory molecule is histone deacetylase ("HDAC").
  • HDAC histone deacetylase
  • the recruiting moiety is an HDAC activator.
  • the HDAC activator is chosen from SAHA and 109 ( Soragni E Front. Neurol. 2015, 6, 44 , and references therein).
  • the regulatory molecule is histone deacetylase ("HDAC").
  • HDAC histone deacetylase
  • the recruiting moiety is an HDAC inhibitor.
  • the HDAC inhibitor is an inositol phosphate.
  • the regulatory molecules is O-linked ⁇ -N-acetylglucosamine transferase ("OGT").
  • the recruiting moiety is an OGT activator.
  • the OGT activator is chosen from ST045849, ST078925, and ST060266 ( Itkonen HM, "Inhibition of O-GlcNAc transferase activity reprograms prostate cancer cell metabolism", Oncotarget 2016, 7(11), 12464-12476 ).
  • the regulatory molecule is chosen from host cell factor 1 ("HCF1") and octamer binding transcription factor (“OCT1").
  • the recruiting moiety is chosen from an HCF1 activator and an OCT1 activator.
  • the recruiting moiety is chosen from VP16 and VP64.
  • the regulatory molecule is chosen from CBP and P300.
  • the recruiting moiety is chosen from a CBP activator and a P300 activator. In certain embodiments, the recruiting moiety is CTPB.
  • the regulatory molecule is P300/CBP-associated factor ("PCAF").
  • the recruiting moiety is a PCAF activator.
  • the PCAF activator is embelin.
  • the regulatory molecule modulates the rearrangement of histones.
  • the regulatory molecule modulates the glycosylation, phosphorylation, alkylation, or acylation of histones.
  • the regulatory molecule is a transcription factor.
  • the regulatory molecule is an RNA polymerase.
  • the regulatory molecule is a moiety that regulates the activity of RNA polymerase.
  • the regulatory molecule interacts with TATA binding protein.
  • the regulatory molecule interacts with transcription factor II D.
  • the regulatory molecule comprises a CDK9 subunit.
  • the regulatory molecule is P-TEFb.
  • the recruiting moiety binds to the regulatory molecule but does not inhibit the activity of the regulatory molecule. In certain embodiments, the recruiting moiety binds to the regulatory molecule and inhibits the activity of the regulatory molecule. In certain embodiments, the recruiting moiety binds to the regulatory molecule and increases the activity of the regulatory molecule.
  • the recruiting moiety binds to the active site of the regulatory molecule. In certain embodiments, the recruiting moiety binds to a regulatory site of the regulatory molecule.
  • the recruiting moiety is chosen from a CDK-9 inhibitor, a cyclin T1 inhibitor, and a PRC2 inhibitor.
  • the recruiting moiety is a CDK-9 inhibitor.
  • the CDK-9 inhibitor is chosen from flavopiridol, CR8, indirubin-3'-monoxime, a 5-fluoro-N2,N4-diphenylpyrimidine-2,4-diamine, a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine, TG02, CDKI-73, a 2,4,5-trisubstited pyrimidine derivatives, LCD000067, Wogonin, BAY-1000394 (Roniciclib), AZD5438, and DRB ( F Morales et al. "Overview of CDK9 as a target in cancer research", Cell Cycle 2016, 15(4), 519-527 , and references therein).
  • the regulatory molecule is a histone demethylase.
  • the histone demethylase is a lysine demethylase.
  • the lysine demethylase is KDM5B.
  • the recruiting moiety is a KDM5B inhibitor.
  • the KDM5B inhibitor is AS-8351 ( N. Cao, Y. Huang, J. Zheng,et al., "Conversion of human fibroblasts into functional cardiomyocytes by small molecules", Science 2016, 352(6290),1216-1220 , and references therein.)
  • the regulatory molecule is the complex between the histone lysine methyltransferases ("HKMT”) GLP and G9A ("GLP/G9A").
  • the recruiting moiety is a GLP/G9A inhibitor.
  • the GLP/G9A inhibitor is BIX-01294 ( Chang Y, "Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294", Nature Struct. Mol. Biol. 2009, 16, 312-317 , and references therein).
  • the regulatory molecule is a DNA methyltransferase ("DNMT").
  • the regulatory moiety is DNMT1.
  • the recruiting moiety is a DNMT1 inhibitor.
  • the DNMT1 inhibitor is chosen from RG108 and the RG108 analogues 1149, T1, and G6. ( B Zhu et al. BioorgMed Chem 2015, 23(12), 2917-2927 and references therein).
  • the recruiting moiety is a PRC1 inhibitor.
  • the PRC1 inhibitor is chosen from UNC4991, UNC3866, and UNC3567 ( JI Stuckey et al. Nature Chem Biol 2016, 12(3), 180-187 and references therein; KD Barnash et al. ACS Chem. Biol. 2016, 11(9), 2475-2483 , and references therein).
  • the recruiting moiety is a PRC2 inhibitor.
  • the PRC2 inhibitor is chosen from A-395, MS37452, MAK683, DZNep, EPZ005687, EI1, GSK126, and UNC1999 ( Konze KD ACS Chem Biol 2013, 8(6), 1324-1334 , and references therein).
  • the recruiting moiety is rohitukine or a derivative of rohitukine.
  • the recruiting moiety is DB08045 or a derivative of DB08045.
  • the recruiting moiety is A-395 or a derivative of A-395.
  • the Oligomeric backbone contains a linker that connects the first terminus and the second terminus and brings the regulatory molecule in proximity to the target gene to modulate gene expression.
  • the length of the linker depends on the type of regulatory protein and also the target gene. In some embodiments, the linker has a length of less than about 50 Angstroms. In some embodiments, the linker has a length of about 20 to 30 Angstroms.
  • the linker comprises between 5 and 50 chain atoms.
  • the oligomeric backbone comprises -(T 1 -V 1 ) a -(T 2 -V 2 ) b -(T 3 -V 3 ) c -(T 4 -V 4 ) d -(T 5 -V 5 ) e -,
  • the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 1. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 2. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 3. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 4. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 5.
  • n is 3-9. In some embodiments, n is 4-8. In some embodiments, n is 5 or 6.
  • T 1 , T 2 , T 3 , and T 4 , and T 5 are each independently selected from (C 1 -C 12 )alkyl, substituted (C 1 -C 12 )alkyl, (EA) w , (EDA) m , (PEG) n , (modified PEG) n , (AA) p , -(CR 2a OH) h -, phenyl, substituted phenyl, piperidin-4-amino (P4A), para-amino-benzyloxycarbonyl (PABC), meta-amino-benzyloxycarbonyl (MABC), para-amino-benzyloxy (PABO), meta-amino-benzyloxy (MABO), paraaminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA) p -MA
  • T 1 , T 2 , T 3 , T 4 and T 5 are each independently selected from (C 1 -C 12 )alkyl, substituted (C 1 -C 12 )alkyl, (EA) w , (EDA) m , (PEG) n , (modified PEG) n , (AA) p ,-(CR 2a OH) h -, optionally substituted (C 6 -C 10 ) arylene, 4-10 membered heterocycloalkene, optionally substituted 5-10 membered heteroarylene.
  • EA has the following structure: and EDA has the following structure:
  • x is 2-3 and q is 1-3 for EA and EDA.
  • R 1a is H or C 1-6 alkyl.
  • T 4 or T 5 is an optionally substituted (C 6 -C 10 ) arylene.
  • T 4 or T 5 is phenylene or substituted phenylene. In some embodiments, T 4 or T 5 is phenylene or phenylene substituted with 1-3 substituents selected from -C 1-6 alkyl, halogen, OH or amine. In some embodiments, T 4 or T 5 is 5-10 membered heteroarylene or substituted heteroarylene. In some embodiments, T 4 or T 5 is 4-10 membered heterocylcylene or substituted heterocylcylene. In some embodiments, T 4 or T 5 is heteroarylene or heterocylcylene optionally substituted with 1-3 substituents selected from -C 1-6 alkyl, halogen, OH or amine.
  • T 1 , T 2 , T 3 , T 4 and T 5 and V 1 , V 2 , V 3 , V 4 and V 5 are selected from the following Table 6: T 1 V 1 T 2 V 2 T 3 V 3 T 4 V 4 T 5 V 5 (C 1 -C 12 ) alkylene CONR 1a (EA) w CO (PEG) n NR 11 CO ---- ---- ---- ---- (C 1 -C 12 ) alkylene CONR 1a (EA) w CO (PEG). O arylene NR 11 CO ---- ---- (C 1 -C 12 ) alkylene CONR 1a (EA) w CO (PEG). O Subst.
  • the linker comprises or any combinations thereof, wherein r is an integer between 1 and 10, preferably between 3 and 7; and X is O, S, or NR 1a . In some embodiments, X is O or NR 1a . In some embodiments, X is O.
  • W' is absent, (CH 2 ) 1-5 , -(CH 2 ) 1-5 O, (CH 2 ) 1-5- C(O)NH-(CH 2 ) 1-5 -O, (CH 2 ) 1-5- C(O)NH-(CH 2 ) 1-5 , -(CH 2 ) 1-5 NHC(O)-(CH 2 ) 1-5 -O, or -(CH 2 ) 1-5 -NHC(O)-(CH 2 ) 1-5 -;
  • E 3 is an optionally substituted C 6-10 arylene group, optionally substituted 4-10 membered heterocycloalkylene, or optionally substituted 5-10 membered heteroarylene;
  • X is O. In some embodiments, X is NH. In some embodiments, E 3 is a C 6-10 arylene group optionally substituted with 1-3 substituents selected from -C 1-6 alkyl, halogen, OH or amine.
  • E 3 is a phenylene or substituted phenylene.
  • the linker comprise a
  • the linker comprises -X(CH 2 ) m (CH 2 CH 2 O) n -, wherein X is -O-, NH-, or - S-, wherein m is 0 or greater and n is at least 1.
  • the linker comprises following the second terminus, wherein R c is selected from a bond, -N(R 1a )-, -O-, and -S-; R d is selected from -N(R 1a )-, -O-, and -S-; and R c is independently selected from hydrogen and optionally substituted C 1-6 alkyl
  • the linker comprises one or more structures selected from , -C 1-12 alkyl, arylene, cycloalkylene, heteroarylene, heterocycloalkylene, -O-, -C(O)NR 1a -,-C(O)-, -NR 1a -, -(CH 2 CH 2 CH 2 O) y -, and -(CH 2 CH 2 CH 2 NR 1a ) y - wherein each d and y are independently 1-10, andeach R 1a is independently hydrogen or C 1-6 alkyl. In some embodiments, d is 4-8.
  • the linker comprises and each d is independently 3-7. In some embodiments, d is 4-6.
  • the linker comprises N(R 1a )(CH 2 ) x N(R 1b )(CH 2 ) x N-, wherein R 1a andR 1b are each independently selected from hydrogen or optionally substituted C 1 -C 6 alkyl; and each x is independently an integer in the range of 1-6..
  • the linker comprises the linker comprises -(CH 2 -C(O)N(R")-(CH 2 ) q -N(R')-(CH 2 ) q -N(R")C(O)-(CH 2 ) x -C(O)N(R")-A-, -(CH 2 ) x -C(O)N(R")-(CH 2 CH 2 O) y (CH 2 ) x -C(O)N(R")-A-, - C(O)N(R")-(CH 2 ) q -N(R')-(CH 2 ) q -N(R")C(O)-(CH 2 ) x -A-, -(CH 2 ) x -O-(CH 2 CH 2 O) y -(CH 2 ) x -N(R")C(O)-(CH 2 ) x -A-, or -N(R")C(O)-
  • the linker is joined with the first terminus with a group selected from - CO-, -NR 1a -,-CONR 1a -, -NR 1a CO-, -CONR 1a C 1-4 alkyl-, -NR 1a CO-C 1-4 alkyl -, -C(O)O-, -OC(O)-, -O-, -S-, -S(O)-, -SO 2 -, -SO 2 NR 1a -, -NR 1 SO 2 -, -P(O)OH-,-((CH2) x -O)-, -((CH 2 ) y -NR 1a -, optionally substituted -C 1-12 alkylene, optionally substituted C 2-10 alkenylene, optionally substituted C 2-10 alkynylene, optionally substituted C 6-10 arylene, optionally substituted C 3-7 cycloalkylene, optionally substituted 5- to 10-membered
  • the linker is joined with the first terminus with a group selected from - CO-, -NR 1a -,C 1-12 alkyl, -CONR 1a -, and -NR 1a CO-.
  • the linker is joined with second terminus with a group selected from —CO—, -NR 1a -,-CONR 1a -, -NR 1a CO-, -CONR 1a C 1-4 alkyl-, -NR 1a CO-C 1-4 alkyl -, -C(O)O-, - OC(O)-, -O-, -S-, -S(O)-, -SO 2 -, -SO 2 NR 1a -, -NR 1 SO 2 -, -P(O)OH-,-((CH 2 ) x -O)-, -((CH 2 ) y -NR 1a )-, optionally substituted -C 1-12 alkylene, optionally substituted C 2-10 alkenylene, optionally substituted C 2-10 alkynylene, optionally substituted C 6-10 arylene, optionally substituted C 3-7 cycloalkylene, optionally substituted 5- to 10-
  • the linker is joined with second terminus with a group selected from —CO—, -NR 1a -, -CONR 1a -, -NR 1a CO-,-((CH 2 ) x -O)-, -((CH 2 ) y -NR 1a )-, -O-, optionally substituted -C 1-12 alkyl, optionally substituted C 6-10 arylene, optionally substituted C 3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene, wherein each x is independently 1-4, each y is independently 1-4, and each R' is independently a hydrogen or optionally substituted C 1-6 alkyl.
  • the compounds comprise a cell-penetrating ligand moiety.
  • the cell-penetrating ligand moiety is a polypeptide.
  • the cell-penetrating ligand moiety is a polypeptide containing fewer than 30 amino acid residues.
  • polypeptide is chosen from any one of SEQ ID NO. 1 to SEQ ID NO. 37, inclusive.
  • the second terminus does not comprise a structure of Formula (C-11): wherein:
  • the protein binding moiety does not have the structure of Formula (C-12): wherein:
  • any compound disclosed above including compounds of Formulas A1-A10, C1-C11, and I - VII, are singly, partially, or fully deuterated. Methods for accomplishing deuterium exchange for hydrogen are known in the art
  • two embodiments are "mutually exclusive" when one is defined to be something which is different than the other.
  • an embodiment wherein two groups combine to form a cycloalkyl is mutually exclusive with an embodiment in which one group is ethyl the other group is hydrogen.
  • an embodiment wherein one group is CH 2 is mutually exclusive with an embodiment wherein the same group is NH.
  • the present disclosure also relates to a method of modulating the transcription of fxn comprising the step of contacting fxn with a compound as described herein.
  • the cell phenotype, cell proliferation, transcription of fxn, production of mRNA from transcription of fxn, translation of fxn, change in biochemical output produced by the protein coded by fxn, or noncovalent binding of the protein coded by fxn with a natural binding partner may be monitored.
  • Such methods may be modes of treatment of disease, biological assays, cellular assays, biochemical assays, or the like.
  • Also provided herein is a method of treatment of a disease mediated by transcription of fxn comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt thereof, to a patient in need thereof.
  • the disease is Friedreich's ataxia.
  • Also provided herein is a compound as disclosed herein for use as a medicament.
  • Also provided herein is a compound as disclosed herein for use as a medicament for the treatment of a disease mediated by transcription of fxn.
  • Also provided herein is a method of modulation of transcription of fxn comprising contacting fxn with a compound as disclosed herein, or a salt thereof.
  • Also provided herein is a method for achieving an effect in a patient comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt thereof, to a patient, wherein the effect is chosen from improved neural sensation, improved vision, improved balance, improved gait, reduced sensitivity to glucose, and reduced sensitivity to carbohydrates.
  • Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 5 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 10 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 20 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 50 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 100 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 200 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 500 or more repeats of GAA.
  • Also provided is a method of modulation of a fxn -mediated function in a subject comprising the administration of a therapeutically effective amount of a compound as disclosed herein.
  • composition comprising a compound as disclosed herein, together with a pharmaceutically acceptable carrier.
  • the pharmaceutical composition is formulated for oral administration.
  • the pharmaceutical composition is formulated for intravenous injection and/or infusion.
  • the oral pharmaceutical composition is chosen from a tablet and a capsule.
  • ex vivo methods of treatment typically include cells, organs, and/or tissues removed from the subject.
  • the cells, organs and/or tissues can, for example, be incubated with the agent under appropriate conditions.
  • the contacted cells, organs, and/or tissues are typically returned to the donor, placed in a recipient, or stored for future use.
  • the compound is generally in a pharmaceutically acceptable carrier.
  • administration of the pharmaceutical composition modulates expression of fxn within 6 hours of treatment. In certain embodiments, administration of the pharmaceutical composition modulates expression of fxn within 24 hours of treatment. In certain embodiments, administration of the pharmaceutical composition modulates expression of fxn within 72 hours of treatment.
  • administration of the pharmaceutical composition causes a 2-fold increase in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 5-fold increase in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 10-fold increase in expression of fxnc9orf72. In certain embodiments, administration of the pharmaceutical composition causes a 20-fold increase in expression of fxn.
  • administration of the pharmaceutical composition causes a 20 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 50 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 80 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 90 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 95 % decrease in expression of fxn2. In certain embodiments, administration of the pharmaceutical composition causes a 99 % decrease in expression of fxn.
  • administration of the pharmaceutical composition causes expression of c9orf72 to fall within 25 % of the level of expression observed for healthy individuals. In certain embodiments, administration of the pharmaceutical composition causes expression of fanto fall within 50 % of the level of expression observed for healthy individuals. In certain embodiments, administration of the pharmaceutical composition causes expression of fxn to fall within 75 % of the level of expression observed for healthy individuals. In certain embodiments, administration of the pharmaceutical composition causes expression of fxn to fall within 90 % of the level of expression observed for healthy individuals.
  • Also provided is a method of modulation of a fxn -mediated function in a subject comprising the administration of a therapeutically effective amount of a compound as disclosed herein.
  • composition comprising a compound as disclosed herein, together with a pharmaceutically acceptable carrier.
  • the pharmaceutical composition is formulated for oral administration.
  • the pharmaceutical composition is formulated for intravenous injection or infusion.
  • the oral pharmaceutical composition is chosen from a tablet and a capsule.
  • ex vivo methods of treatment typically include cells, organs, or tissues removed from the subject.
  • the cells, organs or tissues can, for example, be incubated with the agent under appropriate conditions.
  • the contacted cells, organs, or tissues are typically returned to the donor, placed in a recipient, or stored for future use.
  • the compound is generally in a pharmaceutically acceptable carrier.
  • the compound is effective at a concentration less than about 5 ⁇ M. In certain embodiments, the compound is effective at a concentration less than about 1 ⁇ M. In certain embodiments, the compound is effective at a concentration less than about 400 nM. In certain embodiments, the compound is effective at a concentration less than about 200 nM. In certain embodiments, the compound is effective at a concentration less than about 100 nM. In certain embodiments, the compound is effective at a concentration less than about 50 nM. In certain embodiments, the compound is effective at a concentration less than about 20 nM. In certain embodiments, the compound is effective at a concentration less than about 10 nM.
  • radical naming conventions can include either a mono-radical or a di-radical, depending on the context. For example, where a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical.
  • a substituent identified as alkyl that requires two points of attachment includes di-radicals such as -CH 2 -, -CH 2 CH 2 -, - CH 2 CH(CH 3 )CH 2 -, and the like.
  • Other radical naming conventions clearly indicate that the radical is a di-radical such as "alkylene,” “alkenylene,” “arylene”, “heteroarylene.”
  • R groups are said to form a ring (e.g., a carbocyclyl, heterocyclyl, aryl, or heteroaryl ring) "together with the atom to which they are attached," it is meant that the collective unit of the atom and the two R groups are the recited ring.
  • the ring is not otherwise limited by the definition of each R group when taken individually.
  • R 1 and R 2 are defined as selected from the group consisting of hydrogen and alkyl, or R 1 and R 2 together with the nitrogen to which they are attached form a heterocyclyl
  • R 1 and R 2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure: where ring A is a heteroaryl ring containing the depicted nitrogen.
  • R 1 and R 2 are defined as selected from the group consisting of hydrogen and alkyl, or R 1 and R 2 together with the atoms to which they are attached form an aryl or carbocylyl, it is meant that R 1 and R 2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure: where A is an aryl ring or a carbocylyl containing the depicted double bond.
  • a substituent is depicted as a di-radical (i.e., has two points of attachment to the rest of the molecule), it is to be understood that the substituent can be attached in any directional configuration unless otherwise indicated.
  • polyamide refers to polymers of linkable units chemically bound by amide (i.e., CONH) linkages; optionally, polyamides include chemical probes conjugated therewith.
  • Polyamides may be synthesized by stepwise condensation of carboxylic acids (COOH) with amines (RR'NH) using methods known in the art. Alternatively, polyamides may be formed using enzymatic reactions in vitro, or by employing fermentation with microorganisms.
  • linkable unit refers to methylimidazoles, methylpyrroles, and straight and branched chain aliphatic functionalities (e.g., methylene, ethylene, propylene, butylene, and the like) which optionally contain nitrogen Substituents, and chemical derivatives thereof.
  • the aliphatic functionalities of linkable units can be provided, for example, by condensation of B-alanine or dimethylaminopropylaamine during synthesis of the polyamide by methods well known in the art.
  • linker refers to a chain of at least 10 contiguous atoms. In certain embodiments, the linker contains no more than 20 non-hydrogen atoms. In certain embodiments, the linker contains no more than 40 non-hydrogen atoms. In certain embodiments, the linker contains no more than 60 non-hydrogen atoms. In certain embodiments, the linker contains atoms chosen from C, H, N, O, and S. In certain embodiments, every non-hydrogen atom is chemically bonded either to 2 neighboring atoms in the linker, or one neighboring atom in the linker and a terminus of the linker. In certain embodiments, the linker forms an amide bond with at least one of the two other groups to which it is attached.
  • the linker forms an ester or ether bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms a thiolester or thioether bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms a direct carbon-carbon bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms an amine or amide bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker comprises -(CH 2 OCH 2 )- units. In certain embodiments, the linker comprises -(CH(CH 3 )OCH 2 )- units.
  • turn component refers to a chain of about 4 to 10 contiguous atoms.
  • the turn component contains atoms chosen from C, H, N, O, and S.
  • the turn component forms amide bonds with the two other groups to which it is attached.
  • the turn component contains at least one positive charge at physiological pH.
  • nucleic acid and nucleotide refer to ribonucleotide and deoxyribonucleotide, and analogs thereof, well known in the art.
  • oligonucleotide sequence refers to a plurality of nucleic acids having a defined sequence and length (e.g., 2, 3, 4, 5, 6, or even more nucleotides).
  • oligonucleotide repeat sequence refers to a contiguous expansion of oligonucleotide sequences.
  • RNA i.e., ribonucleic acid
  • modulate transcription refers to a change in transcriptional level which can be measured by methods well known in the art, for example, assay of mRNA, the product of transcription. In certain embodiments, modulation is an increase in transcription. In other embodiments, modulation is a decrease in transcription
  • acyl refers to a carbonyl attached to an alkenyl, alkyl, aryl, cycloalkyl, heteroaryl, heterocycle, or any other moiety were the atom attached to the carbonyl is carbon.
  • An “acetyl” group refers to a -C(O)CH 3 group.
  • An “alkylcarbonyl” or “alkanoyl” group refers to an alkyl group attached to the parent molecular moiety through a carbonyl group. Examples of such groups include methylcarbonyl and ethylcarbonyl. Examples of acyl groups include formyl, alkanoyl and aroyl.
  • alkenyl refers to a straight-chain or branchedchain hydrocarbon radical having one or more double bonds and containing from 2 to 20 carbon atoms. In certain embodiments, said alkenyl will comprise from 2 to 6 carbon atoms.
  • alkoxy refers to an alkyl ether radical, wherein the term alkyl is as defined below.
  • suitable alkyl ether radicals include methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, and the like.
  • alkyl refers to a straight-chain or branchedchain alkyl radical containing from 1 to 20 carbon atoms. In certain embodiments, said alkyl will comprise from 1 to 10 carbon atoms. In further embodiments, said alkyl will comprise from 1 to 8 carbon atoms. Alkyl groups may be optionally substituted as defined herein. Examples of alkyl radicals include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl, noyl and the like.
  • alkylene refers to a saturated aliphatic group derived from a straight or branched chain saturated hydrocarbon attached at two or more positions, such as methylene (-CH 2 -). Unless otherwise specified, the term “alkyl” may include “alkylene” groups.
  • alkylamino refers to an alkyl group attached to the parent molecular moiety through an amino group. Suitable alkylamino groups may be mono- or dialkylated, forming groups such as, for example, N-methylamino, N-ethylamino, N,N-dimethylamino, N,N-ethylmethylamino and the like.
  • alkylidene refers to an alkenyl group in which one carbon atom of the carbon-carbon double bond belongs to the moiety to which the alkenyl group is attached.
  • alkylthio refers to an alkyl thioether (R-S-) radical wherein the term alkyl is as defined above and wherein the sulfur may be singly or doubly oxidized.
  • suitable alkyl thioether radicals include methylthio, ethylthio, n-propylthio, isopropylthio, n-butylthio, iso-butylthio, sec-butylthio, tert-butylthio, methanesulfonyl, ethanesulfinyl, and the like.
  • alkynyl refers to a straight-chain or branched chain hydrocarbon radical having one or more triple bonds and containing from 2 to 20 carbon atoms. In certain embodiments, said alkynyl comprises from 2 to 6 carbon atoms. In further embodiments, said alkynyl comprises from 2 to 4 carbon atoms.
  • alkynylene refers to a carbon-carbon triple bond attached at two positions such as ethynylene (-C:::C-, -C ⁇ C-).
  • alkynyl radicals include ethynyl, propynyl, hydroxypropynyl, butyn-1-yl, butyn-2-yl, pentyn-1-yl, 3-methylbutyn-1-yl, hexyn-2-yl, and the like.
  • alkynyl may include "alkynylene” groups.
  • amido and “carbamoyl,”as used herein, alone or in combination, refer to an amino group as described below attached to the parent molecular moiety through a carbonyl group, or vice versa.
  • C-amido refers to a -C(O)N(RR') group with R and R' as defined herein or as defined by the specifically enumerated “R” groups designated.
  • N-amido refers to a RC(O)N(R')- group, with R and R' as defined herein or as defined by the specifically enumerated "R” groups designated.
  • acylamino as used herein, alone or in combination, embraces an acyl group attached to the parent moiety through an amino group.
  • An example of an “acylamino” group is acetylamino (CH 3 C(O)NH-).
  • amide refers to -C(O)NRR', wherein R and R' are independently chosen from hydrogen, alkyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R' may combine to form heterocycloalkyl, either of which may be optionally substituted.
  • Amides may be formed by direct condensation of carboxylic acids with amines, or by using acid chlorides.
  • coupling reagents are known in the art, including carbodiimide-based compounds such as DCC and EDCI.
  • amino refers to -NRR, wherein R and R are independently chosen from hydrogen, alkyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R' may combine to form heterocycloalkyl, either of which may be optionally substituted.
  • aryl as used herein, alone or in combination, means a carbocyclic aromatic system containing one, two or three rings wherein such polycyclic ring systems are fused together.
  • aryl embraces aromatic groups such as phenyl, naphthyl, anthracenyl, and phenanthryl.
  • arylene embraces aromatic groups such as phenylene, naphthylene, anthracenylene, and phenanthrylene.
  • arylalkenyl or “aralkenyl,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkenyl group.
  • arylalkoxy or “aralkoxy,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkoxy group.
  • arylalkyl or “aralkyl,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkyl group.
  • arylalkynyl or “aralkynyl,” as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkynyl group.
  • arylalkanoyl or “aralkanoyl” or “aroyl,”as used herein, alone or in combination, refers to an acyl radical derived from an aryl-substituted alkanecarboxylic acid such as benzoyl, napthoyl, phenylacetyl, 3-phenylpropionyl (hydrocinnamoyl), 4-phenylbutyryl, (2-naphthyl)acetyl, 4-chlorohydrocinnamoyl, and the like.
  • aryloxy refers to an aryl group attached to the parent molecular moiety through an oxy.
  • carbamate refers to an ester of carbamic acid (-NHCOO-) which may be attached to the parent molecular moiety from either the nitrogen or acid end, and which may be optionally substituted as defined herein.
  • O-carbamyl refers to a -OC(O)NRR', group-with R and R' as defined herein.
  • N-carbamyl as used herein, alone or in combination, refers to a ROC(O)NR'- group, with R and R' as defined herein.
  • carbonyl when alone includes formyl [-C(O)H] and in combination is a - C(O)- group.
  • Carboxyl or “carboxy,” as used herein, refers to -C(O)OH or the corresponding “carboxylate” anion, such as is in a carboxylic acid salt.
  • An "O-carboxy” group refers to a RC(O)O- group, where R is as defined herein.
  • a “C-carboxy” group refers to a -C(O)OR groups where R is as defined herein.
  • cyano as used herein, alone or in combination, refers to -CN.
  • cycloalkyl or, alternatively, “carbocycle,” as used herein, alone or in combination, refers to a saturated or partially saturated monocyclic, bicyclic or tricyclic alkyl group wherein each cyclic moiety contains from 3 to 12 carbon atom ring members and which may optionally be a benzo fused ring system which is optionally substituted as defined herein.
  • said cycloalkyl will comprise from 5 to 7 carbon atoms.
  • cycloalkyl groups examples include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, tetrahydronapthyl, indanyl, octahydronaphthyl, 2,3-dihydro-1H-indenyl, adamantyl and the like.
  • "Bicyclic” and “tricyclic” as used herein are intended to include both fused ring systems, such as decahydronaphthalene, octahydronaphthalene as well as the multicyclic (multicentered) saturated or partially unsaturated type. The latter type of isomer is exemplified in general by, bicyclo[1,1,1]pentane, camphor, adamantane, and bicyclo[3,2,1]octane.
  • esters refers to a carboxy group bridging two moieties linked at carbon atoms.
  • ether refers to an oxy group bridging two moieties linked at carbon atoms.
  • halo or halogen, as used herein, alone or in combination, refers to fluorine, chlorine, bromine, or iodine.
  • haloalkoxy refers to a haloalkyl group attached to the parent molecular moiety through an oxygen atom.
  • haloalkyl refers to an alkyl radical having the meaning as defined above wherein one or more hydrogens are replaced with a halogen. Specifically embraced are monohaloalkyl, dihaloalkyl and polyhaloalkyl radicals.
  • a monohaloalkyl radical for one example, may have an iodo, bromo, chloro or fluoro atom within the radical.
  • Dihalo and polyhaloalkyl radicals may have two or more of the same halo atoms or a combination of different halo radicals.
  • haloalkyl radicals include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl.
  • Haloalkylene refers to a haloalkyl group attached at two or more positions. Examples include fluoromethylene (-CFH-), difluoromethylene (-CF 2 -), chloromethylene (-CHCl-) and the like.
  • heteroalkyl refers to a stable straight or branched chain, or combinations thereof, fully saturated or containing from 1 to 3 degrees of unsaturation, consisting of the stated number of carbon atoms and from one to three heteroatoms chosen from N, O, and S, and wherein the N and S atoms may optionally be oxidized and the N heteroatom may optionally be quatemized.
  • the heteroatom(s) may be placed at any interior position of the heteroalkyl group. Up to two heteroatoms may be consecutive, such as, for example, -CH 2 -NH-OCH 3 .
  • heteroaryl refers to a 3 to 15 membered unsaturated heteromonocyclic ring, or a fused monocyclic, bicyclic, or tricyclic ring system in which at least one of the fused rings is aromatic, which contains at least one atom chosen from N, O, and S.
  • said heteroaryl will comprise from 1 to 4 heteroatoms as ring members.
  • said heteroaryl will comprise from 1 to 2 heteroatoms as ring members.
  • said heteroaryl will comprise from 5 to 7 atoms.
  • heterocyclic rings are fused with aryl rings, wherein heteroaryl rings are fused with other heteroaryl rings, wherein heteroaryl rings are fused with heterocycloalkyl rings, or wherein heteroaryl rings are fused with cycloalkyl rings.
  • heteroaryl groups include pyrrolyl, pyrrolinyl, imidazolyl, pyrazolyl, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazolyl, pyranyl, furyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, thiadiazolyl, isothiazolyl, indolyl, isoindolyl, indolizinyl, benzimidazolyl, quinolyl, isoquinolyl, quinoxalinyl, quinazolinyl, indazolyl, benzotriazolyl, benzodioxolyl, benzopyranyl, benzoxazolyl, benzoxadiazolyl, benzothiazolyl, benzothiadiazolyl, benzofuryl, benzothienyl, chromonyl,
  • Exemplary tricyclic heterocyclic groups include carbazolyl, benzidolyl, phenanthrolinyl, dibenzofuranyl, acridinyl, phenanthridinyl, xanthenyl and the like.
  • heterocycloalkyl and, interchangeably, “heterocycle,” as used herein, alone or in combination, each refer to a saturated, partially unsaturated, or fully unsaturated (but nonaromatic) monocyclic, bicyclic, or tricyclic heterocyclic group containing at least one heteroatom as a ring member, wherein each said heteroatom may be independently chosen from nitrogen, oxygen, and sulfur.
  • said hetercycloalkyl will comprise from 1 to 4 heteroatoms as ring members.
  • said hetercycloalkyl will comprise from 1 to 2 heteroatoms as ring members.
  • said hetercycloalkyl will comprise from 3 to 8 ring members in each ring.
  • said hetercycloalkyl will comprise from 3 to 7 ring members in each ring. In yet further embodiments, said hetercycloalkyl will comprise from 5 to 6 ring members in each ring.
  • "Heterocycloalkyl” and “heterocycle” are intended to include sulfones, sulfoxides, N-oxides of tertiary nitrogen ring members, and carbocyclic fused and benzo fused ring systems; additionally, both terms also include systems where a heterocycle ring is fused to an aryl group, as defined herein, or an additional heterocycle group.
  • heterocycle groups include tetrhydroisoquinoline, aziridinyl, azetidinyl, 1,3-benzodioxolyl, dihydroisoindolyl, dihydroisoquinolinyl, dihydrocinnolinyl, dihydrobenzodioxinyl, dihydro[1,3]oxazolo[4,5-b]pyridinyl, benzothiazolyl, dihydroindolyl, dihy-dropyridinyl, 1,3-dioxanyl, 1,4-dioxanyl, 1,3-dioxolanyl, isoindolinyl, morpholinyl, piperazinyl, pyrrolidinyl, tetrahydropyridinyl, piperidinyl, thiomorpholinyl, and the like.
  • the heterocycle groups may be optionally substituted unless specifically prohibited.
  • hydrazinyl as used herein, alone or in combination, refers to two amino groups joined by a single bond, i.e., -N-N-.
  • hydroxyalkyl refers to a hydroxy group attached to the parent molecular moiety through an alkyl group.
  • isocyanate refers to a -NCO group.
  • isothiocyanato refers to a -NCS group.
  • linear chain of atoms refers to the longest straight chain of atoms independently selected from carbon, nitrogen, oxygen and sulfur.
  • lower means containing from 1 to and including 6 carbon atoms (i.e., C 1 -C 6 alkyl).
  • lower aryl as used herein, alone or in combination, means phenyl or naphthyl, either of which may be optionally substituted as provided.
  • lower heteroaryl means either 1) monocyclic heteroaryl comprising five or six ring members, of which between one and four said members may be heteroatoms chosen from N, O, and S, or 2) bicyclic heteroaryl, wherein each of the fused rings comprises five or six ring members, comprising between them one to four heteroatoms chosen from N, O, and S.
  • lower cycloalkyl as used herein, alone or in combination, means a monocyclic cycloalkyl having between three and six ring members (i.e., C 3 -C 6 cycloalkyl). Lower cycloalkyls may be unsaturated. Examples of lower cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
  • lower heterocycloalkyl as used herein, alone or in combination, means a monocyclic heterocycloalkyl having between three and six ring members, of which between one and four may be heteroatoms chosen from N, O, and S (i.e., C 3 -C 6 heterocycloalkyl).
  • Examples of lower heterocycloalkyls include pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, and morpholinyl.
  • Lower heterocycloalkyls may be unsaturated.
  • lower amino refers to -NRR', wherein R and R are independently chosen from hydrogen and lower alkyl, either of which may be optionally substituted.
  • mercaptyl as used herein, alone or in combination, refers to an RS- group, where R is as defined herein.
  • nitro refers to -NO 2 .
  • perhaloalkoxy refers to an alkoxy group where all of the hydrogen atoms are replaced by halogen atoms.
  • perhaloalkyl refers to an alkyl group where all of the hydrogen atoms are replaced by halogen atoms.
  • sulfonate refers the -SO 3 H group and its anion as the sulfonic acid is used in salt formation.
  • sulfonyl as used herein, alone or in combination, refers to -S(O) 2 -.
  • thia and thio refer to a -S- group or an ether wherein the oxygen is replaced with sulfur.
  • the oxidized derivatives of the thio group namely sulfinyl and sulfonyl, are included in the definition of thia and thio.
  • thiol as used herein, alone or in combination, refers to an -SH group.
  • thiocarbonyl when alone includes thioformyl -e(S)H and in combination is a -e(S)- group.
  • N-thiocarbamyl refers to an ROC(S)NR'- group, with R and R'as defined herein.
  • O-thiocarbamyl refers to a -OC(S)NRR', group with R and R'as defined herein.
  • thiocyanato refers to a -CNS group.
  • trihalomethanesulfonamido refers to a X 3 CS(O) 2 NR- group with X is a halogen and R as defined herein.
  • trihalomethanesulfonyl refers to a X 3 CS(O) 2 - group where X is a halogen.
  • trihalomethoxy refers to a X 3 CO- group where X is a halogen.
  • trimethysilyl as used herein, alone or in combination, refers to a silicone group substituted at its three free valences with groups as listed herein under the definition of substituted amino. Examples include trimethysilyl, tert-butyldimethylsilyl, triphenylsilyl and the like.
  • any definition herein may be used in combination with any other definition to describe a composite structural group.
  • the trailing element of any such definition is that which attaches to the parent moiety.
  • the composite group alkylamido would represent an alkyl group attached to the parent molecule through an amido group
  • the term alkoxyalkyl would represent an alkoxy group attached to the parent molecule through an alkyl group.
  • the term "optionally substituted” means the anteceding group may be substituted or unsubstituted.
  • the substituents of an "optionally substituted” group may include, without limitation, one or more substituents independently selected from the following groups or a particular designated set of groups, alone or in combination: lower alkyl, lower alkenyl, lower alkynyl, lower alkanoyl, lower heteroalkyl, lower heterocycloalkyl, lower haloalkyl, lower haloalkenyl, lower haloalkynyl, lower perhaloalkyl, lower perhaloalkoxy, lower cycloalkyl, phenyl, aryl, aryloxy, lower alkoxy, lower haloalkoxy, oxo, lower acyloxy, carbonyl, carboxyl, lower alkylcarbonyl, lower carboxyester, lower carboxamido, cyano, hydrogen, halogen, hydroxy, amino, lower alkylamino
  • two substituents may be joined together to form a fused five-, six-, or sevenmembered carbocyclic or heterocyclic ring consisting of zero to three heteroatoms, for example forming methylenedioxy or ethylenedioxy.
  • An optionally substituted group may be unsubstituted (e.g., -CH 2 CH 3 ), fully substituted (e.g., -CF 2 CF 3 ), monosubstituted (e.g., -CH 2 CH 2 F) or substituted at a level anywhere inbetween fully substituted and monosubstituted (e.g., -CH 2 CF 3 ).
  • a substituted group is derived from the unsubstituted parent group in which there has been an exchange of one or more hydrogen atoms for another atom or group.
  • substituents independently selected from C 1 -C 6 alkyl, C 1 -C 6 alkenyl, C 1 -C 6 alkynyl, C 1 -C 6 heteroalkyl, C 3 -C 7 carbocyclyl (optionally substituted with halo, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1 -C 6 haloalkyl, and C 1 -C 6 haloalkoxy), C 3 -C 7 -carbocyclyl-C 1 -C 6 -alkyl (optionally substituted with halo, C 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1
  • aryl, heterocycle, R, etc. occur more than one time in a formula or generic structure, its definition at each occurrence is independent of the definition at every other occurrence.
  • certain groups may be attached to a parent molecule or may occupy a position in a chain of elements from either end as written.
  • an unsymmetrical group such as -C(O)N(R)- may be attached to the parent moiety at either the carbon or the nitrogen.
  • Individual stereoisomers of compounds can be prepared synthetically from commercially available starting materials which contain chiral centers or by preparation of mixtures of enantiomeric products followed by separation such as conversion to a mixture of diastereomers followed by separation or recrystallization, chromatographic techniques, direct separation of enantiomers on chiral chromatographic columns, or any other appropriate method known in the art.
  • Starting compounds of particular stereochemistry are either commercially available or can be made and resolved by techniques known in the art.
  • the compounds disclosed herein may exist as geometric isomers. The present disclosure includes all cis, trans, syn, anti,
  • compounds may exist as tautomers; all tautomeric isomers are provided by this disclosure. Additionally, the compounds disclosed herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. In general, the solvated forms are considered equivalent to the unsolvated forms.
  • bonds refers to a covalent linkage between two atoms, or two moieties when the atoms joined by the bond are considered to be part of larger substructure.
  • a bond may be single, double, or triple unless otherwise specified.
  • a dashed line between two atoms in a drawing of a molecule indicates that an additional bond may be present or absent at that position.
  • disease as used herein is intended to be generally synonymous, and is used interchangeably with, the terms “disorder,” “syndrome,” and “condition” (as in medical condition), in that all reflect an abnormal condition of the human or animal body or of one of its parts that impairs normal functioning, is typically manifested by distinguishing signs and symptoms, and causes the human or animal to have a reduced duration or quality of life.
  • combination therapy means the administration of two or more therapeutic agents to treat a therapeutic condition or disorder described in the present disclosure. Such administration encompasses coadministration of these therapeutic agents in a substantially simultaneous manner, such as in a single capsule having a fixed ratio of active ingredients or in multiple, separate capsules for each active ingredient. In addition, such administration also encompasses use of each type of therapeutic agent in a sequential manner. In either case, the treatment regimen will provide beneficial effects of the drug combination in treating the conditions or disorders described herein.
  • terapéuticaally effective is intended to qualify the amount of active ingredients used in the treatment of a disease or disorder or on the effecting of a clinical endpoint.
  • terapéuticaally acceptable refers to those compounds (or salts, prodrugs, tautomers, zwitterionic forms, etc.) which are suitable for use in contact with the tissues of patients without undue toxicity, irritation, and allergic response, are commensurate with a reasonable benefit/risk ratio, and are effective for their intended use.
  • treatment of a patient is intended to include prophylaxis. Treatment may also be preemptive in nature, i.e., it may include prevention of disease. Prevention of a disease may involve complete protection from disease, for example as in the case of prevention of infection with a pathogen, or may involve prevention of disease progression. For example, prevention of a disease may not mean complete foreclosure of any effect related to the diseases at any level, but instead may mean prevention of the symptoms of a disease to a clinically significant or detectable level. Prevention of diseases may also mean prevention of progression of a disease to a later stage of the disease.
  • patient is generally synonymous with the term “subject” and includes all mammals including humans. Examples of patients include humans, livestock such as cows, goats, sheep, pigs, and rabbits, and companion animals such as dogs, cats, rabbits, and horses. Preferably, the patient is a human.
  • prodrug refers to a compound that is made more active in vivo.
  • Certain compounds disclosed herein may also exist as prodrugs, as described in Hydrolysis in Drug and Prodrug Metabolism : Chemistry, Biochemistry, and Enzymology (Testa, Bernard and Mayer, Joachim M. Wiley-VHCA, Zurich, Switzerland 2003 ).
  • Prodrugs of the compounds described herein are structurally modified forms of the compound that readily undergo chemical changes under physiological conditions to provide the compound.
  • prodrugs can be converted to the compound by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to a compound when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.
  • Prodrugs are often useful because, in some situations, they may be easier to administer than the compound, or parent drug. They may, for instance, be bioavailable by oral administration whereas the parent drug is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug.
  • a wide variety of prodrug derivatives are known in the art, such as those that rely on hydrolytic cleavage or oxidative activation of the prodrug.
  • An example, without limitation, of a prodrug would be a compound which is administered as an ester (the "prodrug"), but then is metabolically hydrolyzed to the carboxylic acid, the active entity. Additional examples include peptidyl derivatives of a compound.
  • the compounds disclosed herein can exist as therapeutically acceptable salts.
  • the present disclosure includes compounds listed above in the form of salts, including acid addition salts. Suitable salts include those formed with both organic and inorganic acids. Such acid addition salts will normally be pharmaceutically acceptable. However, salts of non-pharmaceutically acceptable salts may be of utility in the preparation and purification of the compound in question. Basic addition salts may also be formed and be pharmaceutically acceptable.
  • Pharmaceutical Salts Properties, Selection, and Use (Stahl, P. Heinrich. Wiley-VCHA, Zurich, Switzerland, 2002 ).
  • Basic addition salts can be prepared during the final isolation and purification of the compounds by reacting a carboxy group with a suitable base such as the hydroxide, carbonate, or bicarbonate of a metal cation or with ammonia or an organic primary, secondary, or tertiary amine.
  • a suitable base such as the hydroxide, carbonate, or bicarbonate of a metal cation or with ammonia or an organic primary, secondary, or tertiary amine.
  • the cations of therapeutically acceptable salts include lithium, sodium, potassium, calcium, magnesium, and aluminum, as well as nontoxic quaternary amine cations such as ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, diethylamine, ethylamine, tributylamine, pyridine, N , N -dimethylaniline, N -methylpiperidine, N -methylmorpholine, dicyclohexylamine, procaine, dibenzylamine, N , N -dibenzylphenethylamine, 1-ephenamine, and N , N' -dibenzylethylenediamine.
  • Other representative organic amines useful for the formation of base addition salts include ethylenediamine, ethanolamine, diethanolamine, piperidine, and piperazine.
  • compositions of the disclosure may be prepared by any of the well-known techniques of pharmacy, such as effective formulation and administration procedures.
  • Preferred unit dosage formulations are those containing an effective dose, as herein below recited, or an appropriate fraction thereof, of the active ingredient.
  • formulations described above may include other agents conventional in the art having regard to the type of formulation in question, for example those suitable for oral administration may include flavoring agents.
  • the amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration.
  • the compounds can be administered in various modes, e.g. orally, topically, or by injection.
  • the precise amount of compound administered to a patient will be the responsibility of the attendant physician.
  • the specific dose level for any particular patient will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diets, time of administration, route of administration, rate of excretion, drug combination, the precise disorder being treated, and the severity of the indication or condition being treated.
  • the route of administration may vary depending on the condition and its severity. The above considerations concerning effective formulations and administration procedures are well known in the art and are described in standard textbooks.
  • the compounds described herein may be administered at least one of the compounds described herein (or a pharmaceutically acceptable salt thereof) in combination with another therapeutic agent.
  • another therapeutic agent such as one of the side effects experienced by a patient upon receiving one of the compounds herein is hypertension.
  • the therapeutic effectiveness of one of the compounds described herein may be enhanced by administration of an adjuvant (i.e., by itself the adjuvant may only have minimal therapeutic benefit, but in combination with another therapeutic agent, the overall therapeutic benefit to the patient is enhanced).
  • the benefit of experienced by a patient may be increased by administering one of the compounds described herein with another therapeutic agent (which also includes a therapeutic regimen) that also has therapeutic benefit.
  • another therapeutic agent which also includes a therapeutic regimen
  • increased therapeutic benefit may result by also providing the patient with another therapeutic agent for diabetes.
  • the overall benefit experienced by the patient may simply be additive of the two therapeutic agents or the patient may experience a synergistic benefit.
  • the multiple therapeutic agents may be administered in any order or even simultaneously. If simultaneously, the multiple therapeutic agents may be provided in a single, unified form, or in multiple forms (by way of example only, either as a single pill or as two separate pills). One of the therapeutic agents may be given in multiple doses, or both may be given as multiple doses. If not simultaneous, the timing between the multiple doses may be any duration of time ranging from a few minutes to four weeks.
  • certain embodiments provide methods for treating fxn -mediated disorders in a human or animal subject in need of such treatment comprising administering to said subject an amount of a compound disclosed herein effective to reduce or prevent said disorder in the subject, in combination with at least one additional agent for the treatment of said disorder that is known in the art.
  • certain embodiments provide therapeutic compositions comprising at least one compound disclosed herein in combination with one or more additional agents for the treatment of fxn -mediated disorders.
  • certain compounds and formulations disclosed herein may also be useful for veterinary treatment of companion animals, exotic animals and farm animals, including mammals, rodents, and the like. More preferred animals include horses, dogs, and cats.
  • TFA trifluoroacetic acid
  • TFAA trifluoroacetic anhydride
  • THF tetrahydrofuran
  • Tol toluene
  • TsCl tosyl chloride
  • XPhos 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl.
  • polyamides of the present disclosure may be synthesized by solid supported synthetic methods, using compounds such as Boc-protected straight chain aliphatic and heteroaromatic amino acids, and alkylated derivatives thereof, which are cleaved from the support by aminolysis, deprotected (e.g., with sodium thiophenoxide), and purified by reverse-phase HPLC, as well known in the art.
  • the identity and purity of the polyamides may be verified using any of a variety of analytical techniques available to one skilled in the art such as 1 H-NMR, analytical HPLC, or mass spectrometry.
  • Attachment of the linker L and recruiting moiety X can be accomplished with the methods disclosed in Scheme III, which uses a triethylene glycol moiety for the linker L.
  • the mono-TBS ether of triethylene glycol 301 is converted to the bromo compound 302 under Mitsunobu conditions.
  • the recruiting moiety X is attached by displacement of the bromine with a hydroxyl moiety, affording ether 303.
  • the TBS group is then removed by treatment with fluoride, to provide alcohol 304 , which will be suitable for coupling with the polyamide moiety.
  • the amide coupling reagents can be used, but not limited to, are carbodiimides such as dicyclohexylcarbodiimide (DCC), diisopropylcarbodiimide (DIC), ethyl-(N',N'-dimethylamino)propylcarbodiimide hydrochloride (EDC), in combination with reagents such as 1-hydroxybenzotriazole (HOBt), 4-(N,N-dimethylamino)pyridine (DMAP) and diisopropylethylamine (DIEA).
  • DEC dicyclohexylcarbodiimide
  • DIC diisopropylcarbodiimide
  • EDC ethyl-(N',N'-dimethylamino)propylcarbodiimide hydrochloride
  • reagents such as 1-hydroxybenzotriazole (HOBt), 4-(N,N-dimethylamino)pyridine (DMAP)
  • rohitukine-based CDK9 inhibitor A proposed synthesis of a rohitukine-based CDK9 inhibitor is set forth in Scheme V. Synthesis begins with the natural product rohitukine, which is a naturally available compound that has been used as a precursor for CDK9-active drugs such as Alvocidib. The existing hydroxy groups are protected as TBS ethers, the methyl group is brominated, and the bromo compound is coupled with a suitably functionalized linker reagent such as 501 to afford the linked compound 502. Variants of this procedure will be apparent to the person of skill.
  • a proposed synthesis of an A-395 based PRC2 inhibitor is set forth in Scheme VII.
  • the piperidine compound 701 a precursor to A-395, can be reacted with methanesulfonyl chloride 702 to give A-395.
  • 701 is reacted with linked sulfonyl chloride 703 , to provide linked A-395 inhibitor 704
  • the oligomeric backbone is functionalized to adapt to the type of chemical reactions can be performed to link the oligomers to the attaching position in protein binding moieties.
  • the type reactions are suitable but not limited to, are amide coupling reactions, ether formation reactions (O-alkylation reactions), amine formation reactions ( N -alkylation reactions), and sometimes carbon-carbon coupling reactions.
  • the general reactions used to link oligomers and protein binders are shown in below schemes (VIII through X).
  • the compounds and structures shown in Table 2 can be attached to the oligomeric backbone described herein at any position that is chemically feasible while not interfering with the hydrogen bond between the compound and the regulatory protein.
  • Either the oligomer or the protein binder can be functionalized to have a carboxylic acid and the other coupling counterpart being functionalized with an amino group so the moieties can be conjugated together mediated by amide coupling reagents.
  • the amide coupling reagents can be used, but not limited to, are carbodiimides such as dicyclohexylcarbodiimide (DCC), diisopropylcarbodiimide (DIC), ethyl-(N',N'-dimethylamino)propylcarbodiimide hydrochloride (EDC), in combination with reagents such as 1-hydroxybenzotriazole (HOBt), 4-(N,N-dimethylamino)pyridine (DMAP) and diisopropylethylamine (DIEA).
  • DCC dicyclohexylcarbodiimide
  • DIC diisopropylcarbodiimide
  • EDC ethyl-(N',
  • either the oligomer or the protein binder can be functionalized to have an hydroxyl group (phenol or alcohol) and the other coupling counterpart being functionalized with a leaving group such as halide, tosylate and mesylate so the moieties can be conjugated together mediated by a base or catalyst.
  • the bases can be selected from, but not limited to, sodium hydride, potassium hydride, sodium hydroxide, potassium hydroxide, sodium carbonate, potassium carbonate.
  • the catalyst can be selected from silver oxide, phase transfer reagents, iodide salts, and crown ethers.
  • either the oligomer or the protein binder can be functionalized to have an amino group (arylamine or alkylamine) and the other coupling counterpart being functionalized with a leaving group such as halide, tosylate and mesylate so the moieties can be conjugated together directly or with a base or catalyst.
  • the bases can be selected from, but not limited to, sodium hydride, potassium hydride, sodium hydroxide, potassium hydroxide, sodium carbonate, potassium carbonate.
  • the catalyst can be selected from silver oxide, phase transfer reagents, iodide salts, and crown ethers.
  • the alkylation of amines can also be achieved through reductive amination reactions, where in either the oligomer or the protein binder can be functionalized to have an amino group (arylamine or alkylamine) and the other coupling counterpart being functionalized with an aldehyde or ketone group so the moieties can be conjugated together with the treatment of a reducing reagent (hydride source) directly or in combination with a dehydration agent.
  • a reducing reagent hydrogen source
  • the reducing reagents can be selected from, but not limited to, NaBH 4 , NaHB(OAc) 3 , NaBH 3 CN, and dehydration agents are normally Ti(iPrO) 4 , Ti(OEt) 4 , Al(iPrO) 3 , orthoformates and activated molecular sieves.
  • the compounds of the present disclosure comprises a cell-penetrating ligand moiety.
  • the cell-penetrating ligand moiety serves to facilitate transport of the compound across cell membranes.
  • the cell-penetrating ligand moiety is a polypeptide.
  • the Pip5 series is characterized by the sequence ILFQY.
  • the N-terminal cationic sequence contains 1, 2, or 3 substitutions of R for amino acid resides independently chosen from beta-alanine and 6-aminohexanoic acid.
  • the cell-penetrating polypeptide comprises the ILFQY sequence. In certain embodiments, the cell-penetrating polypeptide comprises the QFLY sequence. In certain embodiments, the cell-penetrating polypeptide comprises the QFL sequence.
  • the C-terminal cationic sequence contains 1, 2, or 3 substitutions of R for amino acid resides independently chosen from beta-alanine and 6-aminohexanoic acid.
  • the C-terminal cationic sequence is substituted at every other position with an amino acid residue independently chosen from beta-alanine and 6-aminohexanoic acid.
  • the C-terminal cationic sequence is -HN-RXRBRXRB-COOH. Table 5. Cell-penetrating peptides SEQ ID NO.
  • RXRRBRRXRQFLIRXRBRXRB SEQ ID NO. 31 RXRRBRRXRQFLRXRBRXRB SEQ ID NO. 32 RXRRBRRXYRFLIRXRBRXRB SEQ ID NO. 33 RXRRBRRXRFQILYRXRBRXRB SEQ ID NO. 34 RXRRBRRXYRFRLIXRBRXRB SEQ ID NO. 35 RXRRBRRXILFRYRXRBRXRB SEQ ID NO. 36 Ac-RRLSYSRRRFXBpgG SEQ ID NO.
  • Scheme A describes the steps involved for preparing the polyamide, attaching the polyamide to the oligomeric backbone, and then attaching the ligand to the other end of the oligomeric backbone.
  • the second terminus can include any structure in Table 2.
  • the oligomeric backbone can be selected from the various combinations of linkers shown in Table 6.
  • the transcription modulator molecule such as those listed in Table 7 below can be prepared using the synthesis scheme shown below. Table 6.
  • oligomeric backbone as represented by -(T 1 -V 1 ) a -(T 2 -V 2 ) b -(T 3 -V 3 ) c -(T 4 -V 4 ) d -(T 5 -V 5 ) e - T 1 V 1 T 2 V 2 T 3 V 3 T 4 V 4 T 5 V 5 (alkylene CONR 1a (EA) w CO (PEG) n NR 11 CO ---- ---- ---- ---- (C 1 -C 12 ) alkylene CONR 1a (EA) w CO (PEG) n O arylene NR 11 CO ---- ---- (C 1 -C 12 ) alkylene CONR 1a (EA) w CO (PEG) n O Subst.
  • the ligand or protein binder can be attached to the oligomeric backbone using the schemes described below.
  • the oligomeric backbone can be linked to the protein binder at any position on the protein binder that is chemically feasible while not interfering with the binding between the protein binder and the regulatory protein.
  • the protein binder binds to the regulatory protein often through hydrogen bonds, and linking the oligomeric backbone and the regulatory protein should not interfere the hydrogen bond formation.
  • the protein binder is attached to the oligomeric backbone through an amide or ether bond.
  • Scheme B through Scheme D demonstrate several examples of linking the oligomeric backbone and protein binder.
  • the assays are directed at evaluating the effect of the disclosed compounds on the level of expression of fxn .
  • fxn Expression of fxn will be assayed by techniques known in the field. These assays include, but are not limited to quantitative reverse transcription polymerase chain reaction (RT-PCR), microarray, or multiplexed RNA sequencing (RNA-seq), with the chosen assay measuring either total expression, or the allele specific expression of the fmr gene.
  • RT-PCR quantitative reverse transcription polymerase chain reaction
  • RNA-seq multiplexed RNA sequencing
  • Production of the FMRP protein will be assayed by techniques known in the field. These assays include, but are not limited to Western blot assay, with the chosen assay measuring either total protein expression, or allele specific expression of the fmr gene.
  • tissue models and two animal models are contemplated.
  • This model will constitute patient-derived cells, including fibroblasts, induced pluripotent stem cells and cells differentiated from stem cells. Attention will be made in particular to cell types that show impacts of the disease, e.g., neuronal cell types.
  • This model will constitute cell cultures from mice from tissues that are particularly responsible for disease symptoms, which will include fibroblasts, induced pluripotent stem cells and cells differentiated from stem cells and primary cells that show impacts of the disease, e.g., neuronal cell types.
  • This model wil constitute mice whose genotypes contain the relevant number of repeats for the disease phenotype - these models should show the expected altered gene expression (e.g., a variation in fxn expression).
  • This model will constitute mice whose genotypes contain a knock in of the human genetic locus from a diseased patient - these models should show the expected altered gene expression (e.g., increase or decrease in fxn expression).
  • a transcription modulator molecule having a first terminus, a second terminus, and an oligomeric backbone, wherein:

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Medicinal Chemistry (AREA)
  • Public Health (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Veterinary Medicine (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Epidemiology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Plant Pathology (AREA)
  • Neurology (AREA)
  • Neurosurgery (AREA)
  • Analytical Chemistry (AREA)
  • Oil, Petroleum & Natural Gas (AREA)
  • Hospice & Palliative Care (AREA)
  • Psychiatry (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Pathology (AREA)
  • Immunology (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

Abstract

The present disclosure relates to compounds and methods which may be useful for modulating the expression of fxn and treating diseases and conditions in which fan plays an active role. The compound can be a transcription modulator molecule having a first terminus, a second terminus, and oligomeric backbone, wherein: a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to a nucleotide repeat sequence GAA; b) the second terminus comprises a protein-binding moiety binding to a regulatory molecule that modulates an expression of a gene comprising the nucleotide repeat sequence GAA; and c) the oligomeric backbone comprising a linker between the first terminus and the second terminus.

Description

    CROSS REFERENCE
  • This application claims the benefit of U.S. Application No. 62/674,968, filed May 22, 2018 , which is hereby incorporated by reference in its entirety.
    • FIELD OF INVENTION
  • Disclosed herein are new chimeric heterocyclic polyamide compounds and compositions and their application as pharmaceuticals for the treatment of disease. Methods to modulate the expression of fxn in a human or animal subject are also provided for the treatment diseases such as Friedreich's ataxia.
    • BACKGROUND
  • The disclosure relates to the treatment of inherited genetic diseases characterized by underproduction of mRNA.
  • Friedreich's ataxia (FA or FRDA) is an autosomal recessive neurodegenerative disorder caused by mutations in the fxn gene, which encodes the protein frataxin (FXN), a iron-binding mitochondrial protein involved in electron transport and metabolism. In most subjects with FA, a GAA trinucleotide repeat (from about 66 to over 1000 trinucleotides) is included in the first intron of fxn, and this hyperexpansion is responsible for the observed pathology. Hyperexpansion of the GAA repeats results in reduced expression of FXN.
  • Friedreich's ataxia is characterized by progressive degradation of the nervous system, particularly sensory neurons. In addition, cardiomyocytes and pancreatic beta cells are susceptible to frataxin depletion. Symptoms usually present by age 18; however, later diagnoses of FA are not uncommon. FA patients develop neurodegeneration of the large sensory neurons and spinocerebellar tracts, as well as cardiomyopathy and diabetes mellitus. Clinical symptoms of FA include ataxia, gait ataxia, muscle weakness, loss of upper body strength, loss of balance, lack of reflexes in lower limbs and tendons, loss of sensation, particularly to vibrations, impairment of position sense, impaired perception of temperature, touch, and pain, hearing and vision impairment, including disorted color vision and involuntary eye movements, irregular foot configuration, including pes cavus and inversion, hearing impairment, dysarthria, dysphagia, impaired breathing, scoliosis, diabetes, intolerance to glucose and carbohydrates, cardiac dysfunctions including hypertrophic cardiomyopathy, arrhythmia, myocardial fibrosis, and cardiac failure. Currently there is no cure for FA, with medical treatments being limited to surgical intervention for the spine and the heart, as well as therapy to assist with balance and coordination, motion, and speech.
    • SUMMARY
  • This disclosure utilizes regulatory molecules present in cell nuclei that control gene expression. Eukaryotic cells provide several mechanisms for controlling gene replication, transcription, and/or translation. Regulatory molecules that are produced by various biochemical mechanisms within the cell can modulate the various processes involved in the conversion of genetic information to cellular components. Several regulatory molecules are known to modulate the production of mRNA and, if directed to fxn, would modulate the productionof fxn mRNA that causes Friedreich's ataxia , and thus reverse the progress of the disease.
  • The disclosure provides compounds and methods for recruiting a regulatory molecule into close proximity to fxn. The compounds disclosed herein contain: (a) a recruiting moiety that will bind to a regulatory molecule, linked to (b) a DNA binding moiety that will selectively bind to fxn. The compounds will counteract the expression of defective fxn in the following manner:
    1. (1) The DNA binding moiety will bind selectively the characteristic GAA trinucleotide repeat sequence of fxn;
    2. (2) The recruiting moiety, linked to the DNA binding moiety, will thus be held in proximity to fxn;
    3. (3) The recruiting moiety, now in proximity to fxn, will recruit the regulatory molecule into proximity with the gene; and
    4. (4) The regulatory molecule will modulate expression, and therefore counteract the production of defective fxn by direct interaction with the gene.
  • The mechanism set forth above will provide an effective treatment for Friedreich's ataxia, which is caused by the expression of defective fxn. Correction of the expression of the defective fxn gene thus represents a promising method for the treatment of Friedreich's ataxia.
  • The disclosure provides recruiting moieties that will bind to regulatory molecules. Small molecule inhibitors of regulatory molecules serve as templates for the design of recruiting moieties, since these inhibitors generally act via noncovalent binding to the regulatory molecules.
  • The disclosure further provides for DNA binding moieties that will selectively bind to one or more copies of the GAA trinucleotide repeat that is characteristic of the defective fxn gene. Selective binding of the DNA binding moiety to fxn, made possible due to the high GAA count associated with the defective fxn gene, will direct the recruiting moiety into proximity of the gene, and recruit the regulatory molecule into position to up-regulate gene transcription.
  • The DNA binding moiety will comprise a polyamide segment that will bind selectively to the target GAA sequence. Polyamides have been designed by Dervan and others that can selectively bind to selected DNA sequences. These polyamides sit in the minor groove of double helical DNA and form hydrogen bonding interactions with the Watson-Crick base pairs. Polyamides that selectively bind to particular DNA sequences can be designed by linking monoamide building blocks according to established chemical rules. One building block is provided for each DNA base pair, with each building block binding noncovalently and selectively to one of the DNA base pairs: A/T, T/A, G/C, and C/G.. Following this guideline, trinucleotides will bind to molecules with three amide units, i.e. triamides. In general, these polyamides will orient in either direction of a DNA sequence, so that the 5'-GAA-3' trinucleotide repeat sequence of fxn can be targeted by polyamides selective either for GAA or for AAG. Furthermore, polyamides that bind to the complementary sequence, in this case, TTC or CTT, will also bind to the trinucleotide repeat sequence of fxn and can be employed as well.
  • In principle, longer DNA sequences can be targeted with higher specificity and/or higher affinity by combining a larger number of monoamide building blocks into longer polyamide chains. Ideally, the binding affinity for a polyamide would simply be equal to the sum of each individual monoamide / DNA base pair interaction. In practice, however, due to the geometric mismatch between the fairly rigid polyamide and DNA structures, longer polyamide sequences do not bind to longer DNA sequences as tightly as would be expected from a simple additive contribution. The geometric mismatch between longer polyamide sequences and longer DNA sequences induces an unfavorable geometric strain that subtracts from the binding affinity that would be otherwise expected.
  • The disclosure therefore provides DNA moieties that comprise hexaamide or pentaamide subunits that are connected by flexible spacers. The spacers alleviate the geometric strain that would otherwise decrease binding affinity of a larger polyamide sequence.
  • Disclosed herein are polyamide compounds that can bind to one or more copies of the trinucleotide repeat sequence GAA, and can modulate the expression of the defective fxngene. Treatment of a subject with these compounds will counteract the expression of the defective fxn gene, and this can reduce the occurrence, severity, and/or frequency of symptoms associated with Friedreich's ataxia. Certain compounds disclosed herein will provide higher binding affinity and/or selectivity than has been observed previously for this class of compounds.
    • INCORPORATION BY REFERENCE
  • All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
    • DETAILED DESCRIPTION
  • The transcription modulator molecule described herein represents an interface of chemistry, biology and precision medicine in that the molecule can be programmed to regulate the expression of a target gene containing nucleotide repeat GAA. The transcription modulator molecule contains DNA binding moieties that will selectively bind to one or more copies of the GAA hexanucleotide repeat that is characteristic of the defective fxn gene. The transcription modulator molecule also contains moieties that bind to regulatory proteins. The selective binding of the target gene will bring the regulatory protein into proximity to the target gene and thus downregulates transcription of the target gene. The molecules and compounds disclosed herein provide higher binding affinity and selectivity than has been observed previously for this class of compounds and can be more effective in treating diseases associated with the defective fxn gene.
  • Treatment of a subject with these compounds will modulate the expression of the defective fxn gene, and this can reduce the occurrence, severity, or frequency of symptoms associated with ALS. The transcription modulator molecules described herein recruits the regulatory molecule to modulate the expression of the defective fxn gene and effectively treats and alleviates the symptoms associated with diseases such as Friedreich ataxia.
    • Transcription Modulator Molecule
  • The transcription modulator molecules disclosed herein possess useful activity for modulating the transcription of a target gene having one or more GAArepeats (e.g., fxn), and may be used in the treatment or prophylaxis of a disease or condition in which the target gene (e.g., fxn) plays an active role. Thus, in broad aspect, certain embodiments also provide pharmaceutical compositions comprising one or more compounds disclosed herein together with a pharmaceutically acceptable carrier, as well as methods of making and using the compounds and compositions. Certain embodiments provide methods for modulating the expression of fxn. Other embodiments provide methods for treating a jxn-mediated disorder in a patient in need of such treatment, comprising administering to said patient a therapeutically effective amount of a compound or composition according to the present disclosure. Also provided is the use of certain compounds disclosed herein for use in the manufacture of a medicament for the treatment of a disease or condition ameliorated by the modulation of the expression of fxn.
  • Some embodiments relate to a transcription modulator molecule or compound having a first terminus, a second terminus, and oligomeric backbone, wherein: a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to a nucleotide repeat sequence GAA; b) the second terminus comprises a protein-binding moiety binding to a regulatory molecule that modulates an expression of a gene comprising the nucleotide repeat sequence GAA; and c) the oligomeric backbone comprising a linker between the first terminus and the second terminus. In some embodiments, the second terminus is not a Brd4 binding moiety.
  • In certain embodiments, the compounds have structural Formula I:

            X-L-Y     (I)

    or a salt thereof, wherein:
    • X comprises a is a recruiting moiety that is capable of noncovalent binding to a regulatory moiety within the nucleus;
    • Y comprises a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the trinucleotide repeat sequence GAA; and
    • L is a linker.
  • Certain compounds disclosed herein may possess useful activity for modulating the transcription of fxn, and may be used in the treatment and/or prophylaxis of a disease or condition in which fxn plays an active role. Thus, in broad aspect, certain embodiments also provide pharmaceutical compositions comprising one or more compounds disclosed herein together with a pharmaceutically acceptable carrier, as well as methods of making and using the compounds and compositions. Certain embodiments provide methods for modulating the expression of fxn. Other embodiments provide methods for treating a fxn-mediated disorder in a patient in need of such treatment, comprising administering to said patient a therapeutically effective amount of a compound or composition according to the present disclosure. Also provided is the use of certain compounds disclosed herein for use in the manufacture of a medicament for the treatment of a disease or condition ameliorated by the modulation of the expression of fxn.
  • In certain embodiments, the regulatory molecule is chosen from a bromodomain-containing protein, a nucleosome remodeling factor (NURF), a bromodomain PHD finger transcription factor (BPTF), a teneleven translocation enzyme (TET), methylcytosine dioxygenase (TET1), a DNA demethylase, a helicase, an acetyltransferase, and a histone deacetylase ("HDAC").
  • In some embodiments, the first terminus is Y, and the second terminus is X, and the oligomeric backbone is L.
  • In In certain embodiments, the compounds have structural Formula II:

            X-L-(Y1-Y2-Y3)n-Y0     (II)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • L is a linker;
    • Y1, Y2, and Y3 are internal subunits, each of which comprises a moiety chosen from a heterocyclic ring or a C1-6straight chain aliphatic segment, and each of which is chemically linked to its two neighbors;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; each subunit can noncovalently bind to an individual nucleotide in the GAA repeat sequence;
    • n is an integer between 1 and 200, inclusive; and
    • (Y1-Y2-Y3)n-Y0 combine to form a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the the trinucleotide repeat sequence GAA.
  • In certain embodiments, the compounds of structural Formula II comprise a subunit for each individual nucleotide in the GAA repeat sequence.
  • In certain embodiment, each internal subunit has an amino (-NH-) group and a carboxy (-CO-) group.
  • In certain embodiments, the compounds of structural Formula II comprise amide (-NHCO-) bonds between each pair of internal subunits.
  • In certain embodiments, the compounds of structural Formula II comprise an amide (-NHCO-) bond between L and the leftmost internal subunit.
  • In certain embodiments, the compounds of structural Formula II comprise an amide bond between the rightmost internal subunit and the end subunit.
  • In certain embodiments, each subunit comprises a moiety that is independently chosen from a heterocycle and an aliphatic chain.
  • In certain embodiments, the heterocycle is a monocyclic heterocycle. In certain embodiments, the heterocycle is a monocyclic 5-membered heterocycle. In certain embodiments, each heterocycle contains a heteroatom independently chosen from N, O, or S. In certain embodiments, each heterocycle is independently chosen from pyrrole, imidazole, thiazole, oxazole, thiophene, and furan.
  • In certain embodiments, the aliphatic chain is a C1-6straight chain aliphatic chain. In certain embodiments, the aliphatic chain has structural formula -(CH2)m-, for m chosen from 1, 2, 3, 4, and 5. In certain embodiments, the aliphatic chain is -CH2CH2-.
  • In certain embodiments, each subunit comprises a moiety independently chosen from
    Figure imgb0001
    Figure imgb0002
    Figure imgb0003
    Figure imgb0004
    Figure imgb0005
    Figure imgb0006
    Figure imgb0007
     -NH-benzopyrazinylene-CO-, -NH-phenylene-CO-, -NH-pyridinylene-CO-, -NH-piperidinylene-CO-, -NH-pyrimidinylene-CO-, -NH-anthracenylene-CO-, -NH-quinolinylene-CO-, and
    Figure imgb0008
     wherein Z is H, NH2, C1-6 alkyl, C1-6 haloalkyl or C1-6 alkyl-NH2.
  • In some emebodiments, Py is
    Figure imgb0009
     Im is
    Figure imgb0010
     Hp is
    Figure imgb0011
     Th is
    Figure imgb0012
     Pz is
    Figure imgb0013
     Nt is
    Figure imgb0014
     Tn is
    Figure imgb0015
     Nh is
    Figure imgb0016
     iNt is
    Figure imgb0017
     iIm is
    Figure imgb0018
     HpBi is
    Figure imgb0019
     ImBi is
    Figure imgb0020
     PyBi is
    Figure imgb0021
     Dp is
    Figure imgb0022
     -NH-benzopyrazinylene-CO- is
    Figure imgb0023
     -NH-phenylene-CO- is
    Figure imgb0024
     -NH-pyridinylene-CO- is
    Figure imgb0025
     -NH-piperidinylene-CO- is
    Figure imgb0026
     ,-NH-pyrazinylene-CO- is
    Figure imgb0027
     -NH-anthracenylene-CO- is
    Figure imgb0028
     and -NH-quinolinylene-CO- is
    Figure imgb0029
     In some embodiments, Py is
    Figure imgb0030
     Im is
    Figure imgb0031
     Hp is
    Figure imgb0032
     This
    Figure imgb0033
  • Pz is
    Figure imgb0034
     Nt is
    Figure imgb0035
     Tn is
    Figure imgb0036
     Nh is
    Figure imgb0037
     iNt is
    Figure imgb0038
     and iIm is
    Figure imgb0039
  • In certain embodiments, n is between 1 and 100, inclusive. In certain embodiments, n is between 1 and 50, inclusive. In certain embodiments, n is between 1 and 20, inclusive. In certain embodiments, n is between 1 and 10, inclusive. In certain embodiments, n is between 1 and 5, inclusive. In certain embodiments, n is an integer between 1 and 3, inclusive. In certain embodiments, n is chosen from 1 and 2. In certain embodiments, n is 1.
  • In certain embodiments, n is an integer between 1 and 5, inclusive.
  • In certain embodiments, n is an integer between 1 and 3, inclusive.
  • In certain embodiments, n is an integer between 1 and 2, inclusive.
  • In certain embodiments, n is 1.
  • In certain embodiments, L comprises a C1-6straight chain aliphatic segment.
  • In certain embodiments, L comprises (CH2OCH2)m; and m is an integer between 1 to 20, inclusive. In certain further embodiments, m is an integer between 1 to 10, inclusive. In certain further embodiments, m is an integer between 1 to 5, inclusive.
  • In certain embodiments, the compounds have structural Formula III:

            X-L-(Y1-Y2-Y3)-(W-Y1-Y2-Y3)n-Y0     (III)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • L is a linker;
    • Y1, Y2, and Y3 are internal subunits, each of which comprises a moiety chosen from a heterocyclic ring or a C1-6straight chain aliphatic segment, and each of which is chemically linked to its two neighbors;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor;
    • each subunit can noncovalently bind to an individual nucleotide in the GAA repeat sequence;
    • W is a spacer;
    • n is an integer between 1 and 200, inclusive; and
    • (Y1-Y2-Y3)-(W-Y1-Y2-Y3)n-Y0 combine to form a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the the hexanucleotide repeat sequence GAA.
  • In certain embodiments, Y1-Y2-Y3 is:
    Figure imgb0040
  • In certain embodiments, Y1-Y2-Y3 is:
    Figure imgb0041
  • In certain embodiments, Y1-Y2-Y3 is Im-Py-β.
  • In certain embodiments, Y1-Y2-Y3 is Im-Im-β.
  • In certain embodiments, each Y1-Y2-Y3 is independently chosen from β-Py-Im and β-Im-Im.
  • In certain embodiments, at most one Y1-Y2-Y3 is β-Im-Im.
  • In certain embodiments of the compound of structural Formula III, n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula III, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula III, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula III, n is 1.
  • In certain embodiments, the compounds have structural Formula IV:

            X-L-(Y1-Y2-Y3)-V-(Y4-Y5-Y6)-Y0     (IV)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • Y1, Y2, Y3, Y4, Y5, and Y6 are internal subunits, each of which comprises a moiety chosen from a heterocyclic ring or a C1-6straight chain aliphatic segment, and each of which is chemically linked to its two neighbors;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor;
    • each subunit can noncovalently bind to an individual nucleotide in the GAA repeat sequence;
    • L is a linker;
    • V is a turn component for forming a hairpin turn;
    • n is an integer between 1 and 200, inclusive; and(Y1-Y2-Y3)-V-(Y4-Y5-Y6)-Y0 combine to form a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the the trinucleotide repeat sequence GAA.
  • In certain embodiments of the compound of structural Formula IV, n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula IV, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula IV, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula IV, n is 1.
  • In certain embodiments, V is -HN-CH2CH2CH2-CO-.
  • In certain embodiments, the compounds have structural Formula V:

            X-C(=O)-CH2CH2-(Y1-Y2-Y3)n-NH-Y0     (V)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • each Y1-Y2-Y3 is independently chosen from β-Py-Im and β-Im-Im;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; and
    • n is an integer between 1 and 200, inclusive.
  • In certain embodiments of the compounds of structural Formula V, at most one of Y1-Y2-Y3 is β-Im-Im.
  • In certain embodiments of the compounds of structural Formula V, Y1-Y2-Y3 is β-Py-Im.
  • In certain embodiments of the compound of structural Formula V, n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula V, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula V, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula V, n is 1.
  • In certain embodiments, the compounds have structural Formula VI:
    Figure imgb0042
     or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; and
    • n is an integer between 1 and 200, inclusive.
  • In certain embodiments of the compound of structural Formula VI, n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula VI, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula VI, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula VI, n is 1.
  • In certain embodiments, the compounds have structural Formula VII:
    Figure imgb0043
     or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus; and
    • W is a spacer;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; and
    • n is an integer between 1 and 200, inclusive.
  • In certain embodiments of the compound of structural Formula VII, n is between 1 and 100, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 50, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 20, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 10, inclusive. In certain embodiments of the compound of structural Formula VII, n is between 1 and 5, inclusive. In certain embodiments of the compound of structural Formula VII, n is chosen from 1 and 2. In certain embodiments of the compound of structural Formula VII, n is 1.
  • In certain embodiments of the compounds of structural Formula VII,
    • W is -NHCH2-(CH2OCH2)p-CH2CO-; and
    • p is an integer between 1 and 4, inclusive.
  • In some embodiments, V is -(CH2)a-NR1-(CH2)6-, -(CH2)a-, -(CH2)a-O-(CH2)b-, -(CH2)a-CH(NHR1)-, -(CH2)a-CH(NHR1)-, -{CR2R3)a-, or -(CH2)a-CH(NR1 3)+-(CH2)b-, wherein each a is independently an integer between 2 and 4; R1 is H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, an optionally substituted C6-10 aryl, an optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; each R2 and R3 are independently H, halogen, OH, NHAc, or C1-4 alky. In some embodiments, R1 is H. In some embodiments, R1 is C1-6 alkyl optionally substituted by 1-3 substituents selected from -C(O)-phenyl. In some embodiments, V is -(CR2R3)-(CH2)a- or -(CH2)a-(CR2R3)-(CH2)b-, wherein each a is independently 1-3, b is 0-3, and each R2 and R3 are independently H, halogen, OH, NHAc, or C1-4 alky. In some embodiments, V is -(CH2)- CH(NH3)+-(CH2)- or -(CH2)-CH2CH(NH3)+-.
  • In one aspect, the compounds of the present disclosure bind to the GAAof fxn and recruit a regulatory moiety to the vicinity of fxn. The regulatory moiety, due to its proximity to the gene, will be more likely to modulate the expression of fxn.
  • Also provided are embodiments wherein any compound disclosed above, including compounds of Formulas 1 - VII, are singly, partially, or fully deuterated. Methods for accomplishing deuterium exchange for hydrogen are known in the art.
  • Also provided are embodiments wherein any embodiment above may be combined with any one or more of these embodiments, provided the combination is not mutually exclusive.
  • As used herein, two embodiments are "mutually exclusive" when one is defined to be something which is different than the other. For example, an embodiment wherein two groups combine to form a cycloalkyl is mutually exclusive with an embodiment in which one group is ethyl the other group is hydrogen. Similarly, an embodiment wherein one group is CH2 is mutually exclusive with an embodiment wherein the same group is NH.
  • In one aspect, the compounds of the present disclosure bind to the GAA of fxn and recruit a regulatory moiety to the vicinity of fxn. The regulatory moiety, due to its proximity to the gene, will be more likely to modulate the expression of fxn.
  • In one aspect, the compounds of the present disclosure provide a polyamide sequence for interaction of a single polyamide subunit to each base pair in the GAA repeat sequence. In one aspect, the the compounds of the present disclosure provide a turn component V, in order to enable hairpin binding of the compound to the GAA, in which each nucleotide pair interacts with two subunits of the polyamide.
  • In one aspect, the compounds of the present disclosure provide more than one copy of the polyamide sequence for noncovalent binding to the fxn, and the individual polyamide sequences in this compound are linked by a spacer W, as defined above. The spacer W allows this compound to adjust its geometry as needed to alleviate the geometric strain that otherwise affects the noncovalent binding of longer polyamide sequences.
    • First terminus - DNA binding moiety
  • The first terminus interacts and binds with the gene, particularly with the minor grooves of the GAA sequence. In one aspect, the compounds of the present disclosure provide a polyamide sequence for interaction of a single polyamide subunit to each base pair in the GAA repeat sequence. In one aspect, the compounds of the present disclosure provide a turn component (e.g, aliphatic amino acid moiety), in order to enable hairpin binding of the compound to the GAA, in which each nucleotide pair interacts with two subunits of the polyamide.
  • In one aspect, the compounds of the present disclosure are more likely to bind to the repeated GAA of fxn than to GAA elsewhere in the subject's DNA, due to the high number of GAA repeats associated with fxn.
  • In one aspect, the compounds of the present disclosure provide more than one copy of the polyamide sequence for noncovalent binding to GAA. In one aspect, the compounds of the present disclosure bind to fxnwith an affinity that is greater than a corresponding compound that contains a single polyamide sequence.
  • In one aspect, the compounds of the present disclosure provide more than one copy of the polyamide sequence for noncovalent binding to the GAA, and the individual polyamide sequences in this compound are linked by a spacer W, as defined above. The spacer W allows this compound to adjust its geometry as needed to alleviate the geometric strain that otherwise affects the noncovalent binding of longer polyamide sequences.
  • In certain embodiments, the DNA recognition or binding moiety binds in the minor groove of DNA.
  • In certain embodiments, the DNA recognition or binding moiety comprises a polymeric sequence of monomers, wherein each monomer in the polymer selectively binds to a certain DNA base pair.
  • In certain embodiments, the DNA recognition or binding moiety comprises a polyamide moiety.
  • In certain embodiments, the DNA recognition or binding moiety comprises a polyamide moiety comprising heteroaromatic monomers, wherein each heteroaromatic monomer binds noncovalently to a specific nucleotide, and each heteroaromatic monomer is attached to its neighbor or neighbors via amide bonds.
  • In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 1000 pentanucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 500 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 200 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 100 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 50 trinucleotide repeats. In certain embodiments, the DNA recognition moiety binds to a sequence comprising at least 20 trinucleotide repeats.
  • In certain embodiments, the compounds comprise a cell-penetrating ligand moiety.
  • In certain embodiments, the cell-penetrating ligand moiety is a polypeptide.
  • In certain embodiments, the cell-penetrating ligand moiety is a polypeptide containing fewer than 30 amino acid residues.
  • In certain embodiments, the polypeptide is chosen from any one of SEQ ID NO. 1 to SEQ ID NO. 37, inclusive.
  • The form of the polyamide selected can vary based on the target gene. The first terminus can include a polyamide selected from the group consisting of a linear polyamide, a hairpin polyamide, a H-pin polyamide, an overlapped polyamide, a slipped polyamide, a cyclic polyamide, a tandem polyamide, and an extended polyamide. In some embodiments, the first terminus comprises a linear polyamide. In some embodiments, the first terminus comprises a hairpin polyamide.
  • The binding affinity between the polyamide and the target gene can be adjusted based on the composition of the polyamide. In some embodiments, the polyamide is capable of binding the DNA with an affinity of less than about 600 nM, about 500 nM, about 400 nM, about 300 nM, about 250 nM, about 200 nM, about 150 nM, about 100 nM, or about 50nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity of less than about 300 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity of less than about 200 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity of greater than about 200 nM, about 150 nM, about 100 nM, about 50 nM, about 10 nM, or about 1 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity in the range of about 1-600 nM, 10-500 nM, 20-500 nM, 50-400 nM, or 100-300 nM.
  • The binding affinity between the polyamide and the target DNA can be determined using a quantitative footprint titration experiment. The experiment involve measuring the dissociation constant Kd of the polyamide for target sequence at either 24° C. or 37° C., and using either standard polyamide assay solution conditions or approximate intracellular solution conditions.
  • The binding affinity between the regulatory protein and the ligand on the second terminus can be determined using an assay suitable for the specific protein. The experiment involve measuring the dissociation constant Kd of the ligand for protein and using either standard protein assay solution conditions or approximate intracellular solution conditions.
  • In some embodiments, the first terminus comprises -NH-Q-C(O)-, wherein Q is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene group. In some embodiments, Q is an optionally substituted C6-10 arylene group or optionally substituted 5-10 membered heteroarylene group. In some embodiments, Q is an optionally substituted 5-10 membered heteroarylene group. In some embodiments, the 5-10 membered heteroarylene group is optionally substituted with 1-4 substituents selected from H, OH, halogen, C1-10 alkyl, NO2, CN, NR'R", C1-6 haloalkyl, C1-6 alkoxyl, C1-6 haloalkoxy, (C1-6 alkoxy)C1-6 alkyl, C2-10 alkenyl, C2-10 alkynyl, C3-7 carbocyclyl, 4-10 membered heterocyclyl, C6-10 aryl, 5-10 membered heteroaryl, (C3-7carbocyclyl)C1-6 alkyl, (4-10 membered heterocyclyl)C1-6 alkyl, (C6-10 aryl)C1-6 alkyl, (C6-10 aryl)C1-6 alkoxy, (5-10 membered heteroaryl)C1-6 alkyl, (C3-7carbocyclyl)-amine, (4-10 membered heterocyclyl)amine, (C6-10aryl)amine, (5-10 membered heteroaryl)amine, acyl, C-carboxy, O-carboxy, C-amido, N-amido, S-sulfonamido, N-sulfonamido, -SR', COOH, or CONR'R"; wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, C1-10 alkoxyl.
  • In some embodiments, the first terminus comprises at least three aromatic carboxamide moieties selected to correspond to the nucleotide repeat sequence GAA and at least one aliphatic amino acid residue chosen from the group consisting of glycine, β-alanine, γ-aminobutyric acid, 2,4-diaminobutyric acid, and 5-aminovaleric acid. In some embodiments, the first terminus comprises at least one β-alanine subunit.
  • In some embodiments, the monomer element is independently selected from the group consisting of optionally substituted pyrrole carboxamide monomer, optionally substituted imidazole carboxamide monomer, optionally substituted C-C linked heteromonocyclic/heterobicyclic moiety, and β-alanine.
  • The transcription modulator molecule of claim 1, wherein the first terminus comprises a structure of Formula (A-1):

            -L1a-[A-M]p-E1     (A-1)

    wherein:
    • each [A-M] appears p times and p is an integer in the range of 1 to 10,
    • L1a is a bond, a C1-6 alkylene, -NRa-C1-6 alkylene-C(O)-, -NRaC(O)-, -NRa-C1-6 alkylene, -0-, or -O-C1-6 alkylene;
    • each A is selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, - CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, - S(O)-, -S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, —C(O)-CH=CH—, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene, and
      Figure imgb0044
       -NH- C1-6 alkylene-NH-, -O-C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof, and at least one A is - CONH-;
    • each M is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • E1 is H or -AE-G;
    • AE is absent or NHCO-;
    • G is selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRBRb)C1-5alkylene-NRaRb, C0-4alkylene-NHC(=NH)Ra, and optionally substituted amine; and
    • each Ra and Rb are independently selected from the group consisting of H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, and optionally substituted 5-10 membered heteroaryl.
  • In some embodiments, the first terminus can comprise a structure of Formula (A-2):
    Figure imgb0045
     wherein:
    • L2a is a linker selected from -C1-12 alkylene-CRa, -CH, N, -C1-6 alkylene-N, -C(O)N, -NRa-C1-6 alkylene-CH, -O-C0-6 alkylene-CH,
      Figure imgb0046
      Figure imgb0047
    • each p and q are independently an integer in the range of 1 to 10;
    • each m and n are independently an integer in the range of 0 to 10;
    • each A is independently selected from a bond, C1-10 alkylene, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4 alkylene-, -C(O)O-, -O-, -S-, -S(O)-, -S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, or -C(O)-CH=CH-, and at least one A is CONH-;
    • each M is independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each E1 and E2 are independently H or -AE-G;
    • each AE is independently absent or NHCO;
    • each G is independently selected from the group consisting of C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine; and
    • each Ra and Rb are independently selected from the group consisting of H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, and an optionally substituted 5-10 membered heteroaryl; and
    • each R1a and R1b is independently H, or C1-6 alkyl.
  • In certain embodiments, the integers p and q are 2≦p+q≦20. In some embodiments, p is in the range of about 2 to 10. In some embodiments, p is in the range of about 4 to 8. In some embodiments, q is in the range of about 2 to 10. In some embodiments, q is in the range of about 4 to 8.
  • In certain embodiments, L2a is-C2-8 alkylene-CH,
    Figure imgb0048
     and wherein each m and n is independently an integer in the range of 0 to 10. In certain embodiments, L2a is
    Figure imgb0049
     In some embodiments, L2a is -C2-8 alkylene-CH. In some embodiments, L2a is
    Figure imgb0050
     wherein (m+n) is in the range of about 1 to 4. In some embodiments, L2a is
    Figure imgb0051
     and (m+n) is in the range of about 2 to 5. In some embodiments, L2a is
    Figure imgb0052
     wherein (m+n) is in the range of about 1 to 6.
  • The transcription modulator molecule of claim 1, wherein the first terminus comprises a structure of Formula (A-3):

            -L1a-[A-M]p1-L3a-[M-A]q1-E1     (A-3)

    wherein:
    • L1a is a bond, a C1-6 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, or -O-C0-6 alkylene;
    • L3a is a bond, C1-6 alkylene, -NH-C0-6alkylene-C(O)-, -N(CH3)-C0-6 alkylene, -O-C0-6 alkylene, -(CH2)a-NRa-(CH2)b-, -(CH2)a, -(CH2)a-O-(CH2)b-, -(CH2)a-CH(NHRa)-, -(CH2)a-CH(NHRa)-, -(CR1aR1b)a-, or -(CH2)a-CH(NRaRb)-(CH2)b-;
    • each a and b are independently an integer between 2 and 4;
    • each Ra and Rb are independently selected from H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, and an optionally substituted 5-10 membered heteroaryl;
    • each R1a and R1b is independently H, halogen, OH, NHAc, or C1-4 alkyl;
    • each [A-M] appears p1 times and p1 is an integer in the range of 1 to 10;
    • each [M-A] appears q1 times and q1 is an integer in the range of 1 to 10;
    • each A is selected from a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4lkylene-, -NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, -S(O)-, - S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene, and
      Figure imgb0053
       -NH- C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof, and at least one A is NHCO;
    • each M in each [A-M] and [M-A] unit is independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene; and
    • E1 is selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaR2), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5 alkylene- NRaRb, and C0-4 alkylene-NHC(=NH) Ra.
  • In certain embodiments, the integers p1 and q1 are 2≦p1 +q1≦20.
  • In some embodiments, for Formula (A-1) to (A-4), each A is indepedently a bond, C1-6 alkylene, optionally substituted phenylene, optionally substituted thiophenylene, optionally substituted furanylene, - C1-10 alkylene-C(O)-, -C1-10 alkylene-NH-, -CO-, -NRa-, -CONRa-, -CONRaC1-4alkylene-, - NRaCO-C1-4dkylene-, -C(O)O-, -O-, -S-, C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, -CH=CH-, -NH-N=N-, -NH-C(O)-NH-, -N(CH3)-C1-6 alkylene, and
    Figure imgb0054
     -NH-C1-6 alkylene-NH-, -O-C1-6 alkylene-O-, and any combinations optionally substituted 5-10 membered heteroarylene group. In some embodiments, in Formula (A-1) and (A-3), L1a, is a bond. In some embodiments, in Formula (A-1) and (A-3), L1a is a C1-6 alkylene. In some embodiments, in Formula (A-1) and (A-3), L1a is -NH-C1-6 alkylene-C(O)-. In some embodiments, in Formula (A-1) and (A-3), L1a is - N(CH3)-C1-6alkylene-. In some embodiments, in Formula (A-1) and (A-3), L1a is -O-C0-6alkylene-.
  • In some embodiments, L3a is a bond. In some embodiments, L3a is C1-6 alkylene. In some embodiments, L3a is -NH-C1-6 alkylene-C(O)-. In some embodiments, L3a is -N(CH3)-C1-6 alkylene C(O)-. In some embodiments, L3a is -O-C0-6 alkylene. In some embodiments, L3a is -(CH2)a-NRa-(CH2)b-. In some embodiments, L3a is -(CH2)a-O-(CH2)b-. In some embodiments, L3a is -(CH2)a-CH(NHRa)-. In some embodiments, L3a is -(CH2)a-CH(NHRa)-. In some embodiments, L3a is -(CR1aR1b)a-. In some embodiments, L3a is -(CH2)a-CH(NRaRb)-(CH2)b-.
  • In some embodiments, for Formula (A-1) to (A-4), at least one A is NH and at least one A is C(O). In some embodiments, for Formula (A-1) to (A-4), at least two A is NH and at least two A is C(O). In some embodiments, when M is a bicyclic ring, A is a bond. In some embodiments, at least one A is a phenylene optionally substituted with one or more alkyl. In some embodiments, at least one A is thiophenylene optionally substituted with one or more alkyl. In some embodiments, at least one A is a furanylene optionally substituted with one or more alkyl. In some embodiments, at least one A is (CH2)0-4-CH=CH-(CH2)0-4, preferably -CH=CH-. In some embodiments, at least one A is -NH-N=N-. In some embodiments, at least one A is -NH-C(O)-NH-. In some embodiments, at least one A is -N(CH3)-C1-6 alkylene. In some embodiments, at least one A is
    Figure imgb0055
     In some embodiments, at least one A is -NH- C1-6 alkylene-NH-. In some embodiments, at least one A is -O-C1-6 alkylene-O-.
  • In some embodiments, each M in [A-M] of Formula (A-1) to (A-4) is C6-10 arylene group, 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or C1-6 alkylene; each optionally substituted by 1-3 substituents selected from H, OH, halogen, C1-10 alkyl, NO2, CN, NRaRb, C1-6 haloalkyl, -C1-6 alkoxyl, C1-6 haloalkoxy, (C1-6 alkoxy)C1-6 alkyl, C2-10alkenyl, C2-10alkynyl, C3-7 carbocyclyl, 44-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, -(C3-7carbocyclyl)C1-6alkyl, (4-10 membered heterocyclyl)C1-6alkyl, (C6-10aryl)C1-6alkyl, (C6-10aryl)C1-6alkoxy, (5-10 membered heteroaryl)C1-6alkyl, -(C3-7carbocyclyl)-amine, (4-10 membered heterocyclyl)amine, (C6-10aryl)amine, (5-10 membered heteroaryl)amine, acyl, C-carboxy, O-carboxy, C-amido, N-amido, S-sulfonamido, N-sulfonamido, -SR', COOH, or CONRaRb; wherein each Ra and Rb are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl. In some embodiments, each M in [A-M] of Formula (A-1) to (A-3) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N or a C1-6 alkylene, and the heteroarylene or the a C1-6 alkylene is optionally substituted with 1-3 substituents selected from OH, halogen, C1-10 alkyl, NO2, CN, NRaRb, C1-6haloalkyl, -C1-6alkoxyl, C1-6haloalkoxy, C3-7carbocyclyl, 4-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, -SR', COOH, or CONRaRb; wherein each Ra and Rb are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl. In some embodiments, each R in [A-R] of Formula (A-1) to (A-3) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N, and the heteroarylene is optionally substituted with 1-3 substituents selected from OH, C1-6 alkyl, halogen, and C1-6 alkoxyl.
  • In some embodiments, for Formula (A-1) to (A-4), at least one M is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one M is a pyrrole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one M is a immidazole optionally subsituted with one or more C1-10 alkyl. In some embodiments, for Formula (A-1) to (A-4), at least one M is a C2-6 alkylene optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one M is a pyrrole optionally subsituted with one or more C1-10 alkyl. In some embodiments, for Formula (A-1) to (A-4), at least one M is a bicyclic heteroarylene or arylene. In some embodiments, at least one M is a phenylene optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one M is a benzimmidazole optionally subsituted with one or more C1-10 alkyl.
  • In some embodiments, the first terminus comprises a structure of Formula (A-4):
    Figure imgb0056
     wherein:
    • L1c is a bivalent or trivalent group selected from
      Figure imgb0057
      Figure imgb0058
       a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
      Figure imgb0059
    • p is an integer in the range of 3 to 10; 2 ≦ q ≦ p − 1 ;
      Figure imgb0060
       2 ≦ r ≦ p − 1 ;
      Figure imgb0061
    • m and n are each independently an integer in the range of 0 to 10;
    • each A2 through Ap is independently selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-,-C1-10alkylene-NRa-, -CO-, -NRa-,-CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene, -C(O)O-, -O-, -S-, -S(O)-, -S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene,
      Figure imgb0062
       -NH- C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof, and at least one A2 through Ap is NHCO;
    • each M1 through Mp is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each T2 through Tp is independently selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-,-C1-10 alkylene-NRa-, -CO-, -NRa-,-CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene, -C(O)O-, -O-, -S-, -S(O)-, -S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene,
      Figure imgb0063
       -NH- C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, and -NH-C(O)-NH-, and any combinations thereof,
    • each Q1 to Qp is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each A1, A2, E1, and E2 are indpendently H or -AE-G;
    • each AE is independently absent or NHCO;
    • each G is independently selected from the group consisting of optionally substituted H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • when L1c is a trivalent group, the oligomeric backbone is attached to the first terminus through L1c, and each G is an end group independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylcne-NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • when L1c is a divalent group, the oligomeric backbone is attached to the first terminus through one of A1, T1, E1, and E2, and each G is independently selected from the group consisting of a bond, a -C1-6 alkylene-, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, -C(O)-, -C(O)-C1. 10alkylene, and -O-C0-6 alkylene, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH)Ra, and optionally substituted amine; or
    • when L1c is a bivalent group, the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of M1, M2, ...Mp-1, Mp, T1, T2, ...Tp-1, and Tp, and each G is an end group independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH)Ra, and optionally substituted, and
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl;
      each R1a and R1b are independently H or an optionally substituted C1-6 alkyl.
  • In some embodiments, the first terminus comprises a structure of Formula (A-4a) or (A-4b):
    Figure imgb0064
     or
    Figure imgb0065
     wherein:
    • L1c is a bivalent or trivalent group selected from
      Figure imgb0066
      Figure imgb0067
       a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
      Figure imgb0068
    • p is an integer in the range of 2 to 10;
    • p' is an integer in the range of 2 to 10; 2 ≦ q ≦ p − 1 ;
      Figure imgb0069
       2 ≦ r ≦ p − 1 ;
      Figure imgb0070
    • m and n are each independently an integer in the range of 0 to 10;
    • each A2 through Ap is independently selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-,-C1-10 alkylene-NRa-, -CO-, -NRa-,-CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene, -C(O)O-, -O-, -S-, -S(O)-, -S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene, and
      Figure imgb0071
       -NH-C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof, and at least one of A2 through Ap is -CONH-;
    • each M1 through Mp is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each T2 through Tp' in formula (A-4a) is independently selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-,-NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, -S(O)-, -S(O)2-, -C(=S)-NH-,-C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene, and
      Figure imgb0072
       -NH- C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof, and at least one of T2 through Tp is -CONH-;
    • each Q1 to Qp' is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each A1, T1, E1, and E2 are independently H or -AE-G,
    • each AE is independently absent or NHCO,
    • each G is independently selected from the group consisting of optionally substituted H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • when L1c is a trivalent group, the oligomeric backbone is attached to the first terminus through L1c, when L1c is a bivalent group, the oligomeric backbone is attached to the first terminus through one of A1, T1, E1, and E2, or the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of M1, M2, ...Mp-1, NP, T1, T2, ...Tp'-1, and Tp', and
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl;
    • each R1a and R1b are independently H or an optionally substituted C1-6 alkyl
  • In certain embodiments, L1c is
    Figure imgb0073
     C1-10 alkylene, or
    Figure imgb0074
     In certain embodiments, L1c is C3-8 alkylene. In certain embodiments, L1c is
    Figure imgb0075
     and wherein 2≦m+n≦10. In some embodiments, L1c is C2-8 alkylene. In some embodiments, L1c is C3-8 alkylene. In some embodiments, L1c is C4-8 alkylene. In some embodiments, L1c is C3 alkylene, C4 alkylene, C5 alkylene, C6 alkylene, C7 alkylene, C8 alkylene, or C9 alkylene.
  • In certain embodiments, 3≦m+n≦7. In certain embodiments, (m+n) is 3, 4, 5, 6, 7, 8, or 9. In certain embodiments, m is in the range of 3 to 8. In certain embodiments, m is 3, 4, 5, 6, 7, 8, or 9.
  • In certain embodiments, Mq is a five to 10 membered heteroaryl ring comprising at least one nitrogen; Qq is a five to 10 membered heteroaryl ring comprising at least one nitrogen; and Mq is linked to Qq through L1c.In certain embodiments, Mq is a five membered heteroaryl ring comprising at least one nitrogen; Qq is a five membered heteroaryl ring comprising at least one nitrogen; Mq is linked to Qq through L1c, and L1c is attached to the nitrogen atom on Mq and L1c is attached to the nitrogen atom on Qq.
  • In certain embodiments, each M1 through Mp is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C1-6 alkylene.
  • In certain embodiments, at least one M of M1 through Mp is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least two M of M1 through Mp is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least three, four, five, or six M of M1 through Mp is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one of M1 through Mp is a pyrrole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of M1 through Mp is a immidazole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of M1 through Mp is a C2-6 alkylene optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one of M1 through Mp is a phenyl optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of M1 through Mp is a bicyclic heteroarylene or arylene. In some embodiments, at least one of M1 through Mp is a phenylene optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of M1 through Mp is a benzimmidazole optionally subsituted with one or more C1-10 alkyl.
  • In certain embodiments, each Q1 to Qp is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C1-6 alkylene.
  • In certain embodiments, at least one Q of Q1 through Qp is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least two Q of Q1 through Qp is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least three, four, five, or six Q of Q1 through Qp is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one of Q1 through Qp is a pyrrole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Q1 through Qp is a immidazole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Q1 through Qp is a C2-6 alkylene optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one of Q1 through Qp is a phenyl optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Q1 through Qp is a bicyclic heteroarylene or arylene. In some embodiments, at least one of Q1 through Qp is a phenylene optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Q1 through Qp is a benzimmidazole optionally subsituted with one or more C1-10 alkyl.
  • In some embodiments, at least one of A2 through Ap is NH and at least one of A2 through Ap is C(O). In some embodiments, at least two of A2 through Ap is NH and at least two of A2 through Ap is C(O). In some embodiments, when one of M2 through Mp is a bicyclic ring, the adjacent A is a bond. In some embodiments, one of A2 through Ap is a phenylene optionally substituted with one or more alkyl. In some embodiments, one of A2 through Ap is thiophenylene optionally substituted with one or more alkyl. In some embodiments, one of A2 through Ap is a furanylene optionally substituted with one or more alkyl. In some embodiments, one of A2 through Ap is (CH2)0-4-CH=CH-(CH2)0-4, preferably -CH=CH-. In some embodiments, one of A2 through Ap is -NH-N=N-. In some embodiments, one of A2 through Ap is -NH-C(O)-NH-. In some embodiments, one of A2 through Ap is -N(CH3)-C1-6 alkylene. In some embodiments, one of A2 through Ap is
    Figure imgb0076
     In some embodiments, one of A2 through Ap is -NH- C1-6 alkylene-NH-. In some embodiments, one of A2 through Ap is -O-C1-6 alkylene-O-.
  • In certain embodiments, each A2 through Ap is independently selected from a bond, C1-10 alkylene, optionally substituted phenylene, optionally substituted thiophenylene, optionally substituted furanylene, - C1-10 alkylene-C(O)-, -C1-10 alkylene-NH-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, - NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, —C(O)-CH=CH—, -CH=CH-, -NH-N=N-, -NH-C(O)-NH-, -N(CH3)-C1-6 alkylene,
    Figure imgb0077
     -NH- C1-6 alkylene-NH-, and -O-C1-6 alkylene-O-, and any combinations thereof.
  • In some embodiments, at least one T of T2 through Tp is NH and at least one of T of T2 through Tp is C(O). In some embodiments, at least two T of T2 through Tp is NH and at least two T of T2 through Tp is C(O). In some embodiments, when one Q of Q2 through Qp is a bicyclic ring, the adjacent T is a bond. In some embodiments, one T of T2 through Tp is a phenylene optionally substituted with one or more alkyl. In some embodiments, one T of T2 through Tp is thiophenylene optionally substituted with one or more alkyl. In some embodiments, one T of T2 through Tp is a furanylene optionally substituted with one or more alkyl. In some embodiments, one T of T2 through Tp is (CH2)0-4-CH=CH-(CH2)0-4, preferably -CH=CH-. In some embodiments, one T of T2 through Tp is -NH-N=N-. In some embodiments, one T of T2 through Tp is -NH-C(O)-NH-. In some embodiments, one T of T2 through Tp is -N(CH3)-C1-6 alkylene. In some embodiments, one T of T2 through Tp is
    Figure imgb0078
     In some embodiments, one T of T2 through Tp is -NH- C1-6 alkylene-NH-. In some embodiments, one T of T2 through Tp is -O-C1-6 alkylene-O-.
  • In certain embodiments, each T2 through Tp is independently selected from a bond, C1-10 alkylene, optionally substituted phenylene, optionally substituted thiophenylene, optionally substituted furanylene, - C1-10 alkylene-C(O)-, -C1-10 alkylene-NH-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, - NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, —C(O)-CH=CH—, -CH=CH-, -NH-N=N-, -NH-C(O)-NH-, -N(CH3)-C1-6 alkylene, and
    Figure imgb0079
     -NH-C1-6 alkylene-NH-, -O-C1-6 alkylene-0-, and any combinations thereof.
  • In certain embodiments, each A1, T1, E1, and E2 are independently -AE-G, and each AE is independently absent or NHCO. In certain embodiments, each A1, T1, E1, and E2 are independently -AE-G and each AE is independently NHCO.
  • In certain embodiments, for Formula (A-1) to (A-4), each end group G independently comprises a moiety selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, a 5-10 membered heteroaryl optionally substituted with 1-3 substituents selected from C1-6 alkyl, -NHCOH, halogen, -NRaRb, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, C0-4 alkylene-NHC(=NH)-RE, -C1-4 alkylene-RE, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5 alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine, wherein each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl. In certain embodiments, for Formula (A-1) to (A-4), each end group G independently comprises a NH or CO group. In certain embodiments, each Ra and Rb are independently H or C1-6 alkyl. In certain embodiments, for formula (A-1) to (A-4), at least one of the end groups is H. In certain embodiments, for Formula (A-1) to (A-4), at least two of the end groups are H. In certain embodiments, for formula (A-1) to (A-4), at least one of the end groups is H. In certain embodiments, for Formula (A-1) to (A-4), at least one of the end groups is -NH-5-10 membered heteroaryl ring optionally substituted with one or more alkyl or -CO-5-10 membered heteroaryl ring optionally substituted with one or more alkyl.
  • In certain embodiments, for Formula (A-1) to (A-4), each end group G is independently selected from C1-4alkylNHC(NH)NH2,
    Figure imgb0080
     -C(=NH)(NH2),
    Figure imgb0081
    Figure imgb0082
    Figure imgb0083
    Figure imgb0084
    Figure imgb0085
    Figure imgb0086
    Figure imgb0087
    Figure imgb0088
  • In certain embodiments, for Formula (A-1) to (A-4), each E1 independently comprises an optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted imidazole containing moiety, or optionally substituted amine.
  • In certain embodiments, for Formula (A-1) to (A-4), each E2 independently comprises an optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted imidazole containing moiety, or optionally substituted amine
  • In certain embodiments, for Formula (A-1) to (A-4), each E1 and E2 independently comprises a moiety selected from the group consisting of optionally substituted N-methylpyrrole, optionally substituted N-methylimidazole, optionally substituted benzimidazole moiety, and optionally substituted 3-(dimethylamino)propanamidyl. In certain embodiments, each E1 and E2 independently comprises thiophene, benzothiophene, C-C linked benzimidazole/thiophene-containing moiety, or C-C linked hydroxybenzimidazole/thiophene-containing moiety. In certain embodiments, for Formula (A-1) to (A-4), each E1 and E2 independently also comprises NH or CO group.
  • In certain embodiments, for Formula (A-1) to (A-4), each E1 or E2 independently comprises a moiety selected from the group consisting of isophthalic acid; phthalic acid; terephthalic acid; morpholine; N,N-dimethylbenzamide; N,N-bis(trifluoromethyl)benzamide; fluorobenzene; (trifluoromethyl)benzene; nitrobenzene; phenyl acetate; phenyl 2,2,2-trifluoroacetate; phenyl dihydrogen phosphate; 2H-pyran; 2H-thiopyran; benzoic acid; isonicotinic acid; and nicotinic acid; wherein one, two, or three ring members in any of the end-group candidates can be independently substituted with C, N, S or O; and where any one, two, three, four or five of the hydrogens bound to the ring can be substituted with R3a, wherein R5 may be independently selected from H, OH, halogen, C1-10 alkyl, NO2, NH2, C1-10 haloalkyl, -OC1-10 haloalkyl, COOH, and CONR1cR1d; wherein each R1c and R1d are independently H, C1-10 alkyl, C1-10 haloalkyl, or -C1-10 alkoxyl.
  • In some embodiments, the first terminus comprises the structure of Formula (A-5a) or Formula (A-5b):

            A1a-NH-Q1-C(O)-NH-Q2-C(O)-NH-Q3-C(O)... -NH-Qp-1C(O)-NH-C(O)NH-G     (A-Sa)

    or

            T1a-C(O)-Q1-NH-C(O)-Q2NH-C(O)-Q3-NH-... -C(O)-Qp-1NH-C(O)-Qp-NHC(O)-G     (A-5b)

    wherein:
    • each Q1, Q2, Q3... through Qp are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each A1a and T1a are independently a bond, H, a -C1-6 alkylene-, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, -C(O)-, -C(O)-C1-10alkylene, and -O-C0-6 alkylene, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NHaWb), -C0-4alkylene-C(=N+H2)(NRaRb)Cl-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • p is an integer between 2 and 10; and
    • G is selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, or an optionally substituted alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NHaWb), -C0-4alkylene-C(=N+H2)(NRaRb)Cl-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; and
    • wherein the first terminus is connected to the oligomeric backbone through either A1 or T1, or a nitrogen or carbon atom on one of Q1 through Qp.
  • In certain embodiments, the first terminus comprises the structure of Formula (A-5c):
    Figure imgb0089
     wherein:
    • each Qa 1, Qa 2...Qa q...through Qa p are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each Qb1,Qb 2...Qb r....through Qb p are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • p is an integer between 3 and 10; 2 ≦ q ≦ p − 1 ;
      Figure imgb0090
       2 ≦ r ≦ p − 1 ;
      Figure imgb0091
    • La is selected from a divalent or trivalent group selected from the group consisting of
      Figure imgb0092
      Figure imgb0093
       a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
      Figure imgb0094
    • each m and n are independently an integer in the range of 1 to 10;
    • n is an integer in the range of 1 to 10;
    • each R1a and R1b are independently H, or C1-6 alkyl;
    • when La is a trivalent group, the oligomeric backbone is attached to the first terminus through La, and each W,', Ga, Gb, and Wb 1 are end groups independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • when La is a divalent group, the oligomeric backbone is attached to the first terminus through one of Wa 1, Ga, Gb, and Wb 1, and each Wa 1, Ga, Gb, and Wb 1 are independently selected from the group consisting of a bond, a -C1-6 alkylene-, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, - C(O)-, -C(O)-C1-10alkylene, and -0-C0-6 alkylene, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine; or
    • when La is a bivalent group, the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of Qa 1, Qa 2, ... Qa p-1, Qa p, Qb 1, Qa 2, ... Qb p-1, and Qb p, and each Wa 1, Ga, Gb, and Wb 1 are end groups independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine and
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl.
  • In some embodiments, the first terminus comprises the structure of Formula (A-5c) or (A-5d):
    Figure imgb0095
     or
    Figure imgb0096
     wherein:
    • each Qa 1, Qa 2... Qa q...through Qa p are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each Qb 1,Qb 2...Qb r....through Qb p' are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • p and p' are independently an integer between 3 and 10; 2 ≦ q ≦ p − 1 ;
      Figure imgb0097
       2 ≦ r ≦ p − 1 ;
      Figure imgb0098
    • La is selected from a divalent or trivalent group selected from the group consisting of
      Figure imgb0099
      Figure imgb0100
       a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
      Figure imgb0101
    • each m and n are independently an integer in the range of 1 to 10;
    • n is an integer in the range of 1 to 10;
    • each R1a and R1b are independently H, or C1-6 alkyl;
    • each Wa 1 Ga, Gb, and Wb 1 are end groups independently selected from the group consisting of optionally substituted H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • when La is a trivalent group, the oligomeric backbone is attached to the first terminus through La; and when La is a divalent group, the oligomeric backbone is attached to the first terminus through one of Wa 1, Ea, Eb, and Wb 1, or the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of Qa 1, Qa 2, ... Qa p-1, Qa p, Qb 1, Qa 2, ... Qb p'-1, and Qb p'; and
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl.
  • In certain embodiements of Formula (A-5c)-(A-5d), La is a C2-8 alkylene. In certain embodiments, L6 is C3-8 alkylene. In certain embodiments, La is
    Figure imgb0102
     and wherein 2≦m+n≦10. In some embodiments, La is C4-8 alkylene. In some embodiments, La is C3-7 alkylene. In some embodiments, La is C3 alkylene, C4 alkylene, C5 alkylene, C6 alkylene, C7 alkylene, C8 alkylene, or C9 alkylene.
  • In certain embodiments, for Formula (A-5c)-(A-5d), 3≦m+n≦7. In certain embodiments, (m+n) is 3, 4, 5, 6, 7, 8, or 9. In certain embodiments, m is in the range of 3 to 8. In certain embodiments, m is 3, 4, 5, 6, 7, 8, or 9. In certain embodiments, for Formula (A-5c), p is 2-10. In certain embodiments, for formula (A-5c), p is 3-8. In certain embodiments, for formula (A-5c), p is 2, 3, 4, 5, 6, 7, or 8. In certain embodiments, for Formula (A-5c), q is 2-5. In certain embodiments, for formula (A-5c), p is 2-4. In certain embodiments, for Formula (A-5c), p is 2, 3, 4, 5, or 6.
  • In certain embodiments, Qa q is a five to 10 membered heteroaryl ring comprising at least one nitrogen; Qb q' is a five to 10 membered heteroaryl ring comprising at least one nitrogen; and Qa q is linked to Qb r through La.In certain embodiments, Qa q is a five membered heteroaryl ring comprising at least one nitrogen; Qb r is a five membered heteroaryl ring comprising at least one nitrogen; Qa q is linked to Qb r through La, and La is attached to the nitrogen atom on Qa q and L1c is attached to the nitrogen atom on Qb r.
  • In certain embodiments, each Qa 1 through Qa p is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C1-6 alkylene.
  • In certain embodiments, at least one Q of Qa 1 through Qa p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least two Q of Qa 1 through Qa p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least three, four, five, or six Q of Qa 1 through Qa p is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one Q of Qa 1 through Qa p is a pyrrole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Q of Qa 1 through Qa p is a immidazole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one Q of Qa 1 through Qa p is a C2-6 alkylene optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one Q of Qa 1 through Qa p is a phenyl optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one Q of Qa 1 through Qa p is a bicyclic heteroarylene or arylene. In some embodiments, at least one Q of Qa 1 through Qa p is a phenylene optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one Q of Qa 1 through Qa p is a benzimmidazole optionally subsituted with one or more C1-10 alkyl.
  • In certain embodiments, each Qb1 through Qb p is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C1-6 alkylene.
  • In certain embodiments, at least one Q of Qb 1 through Qb p' is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least two Q of Qb 1 through Qb p' is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In certain embodiments, at least three, four, five, or six Q of Qb 1 through Qb p' is a 5 membered heteroarylene having at least one heteroatom selected from O, N, S and optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one of Qb 1 through Qb p' is a pyrrole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Qb 1 through Qb p' is a immidazole optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Qb 1 through Qb p' is a C2-6 alkylene optionally substituted with one or more C1-10 alkyl. In some embodiments, at least one of Qb 1 through Qb p' is a phenyl optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Qb 1 through Qbp' is a bicyclic heteroarylene or arylene. In some embodiments, at least one of Qb 1 through Qb p' is a phenylene optionally subsituted with one or more C1-10 alkyl. In some embodiments, at least one of Qb 1 through Qb p' is a benzimmidazole optionally subsituted with one or more C1-10 alkyl.
  • In certain embodiments, for Formula (A-5c), each end group Ga, Gb, Wa1, and Wb 1 is independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, a 5-10 membered heteroaryl optionally substituted with 1-3 substituents selected from C1-6 alkyl, -NHCOH, halogen, -NRaRb, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, C0-4 alkylene-NHC(=NH)-Ra, -C1-4 alkylene-Ra, -CN, -C0-4alkylene-C(=NH)(NRaRb ), -C0-6alkylene-C(=N+H2)(NRaRb)C1-5 alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine, wherein each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl. In certain embodiments, each Ra and Rb are independently H or C1-6 alkyl. In certain embodiments, at least one of the end groups is 5-10 membered heteroaryl optionally substituted with C1-6 alkyl, COOH, or OH. In certain embodiments, at least two of the end groups are 5-10 membered heteroaryl optionally substituted with C1-6 alkyl, COOH, or OH. In certain embodiments, for Formula (A-1) to (A-5d), at least one of the end groups is 5-10 membered heteroaryl optionally substituted with C1-6 alkyl, COOH, or OH. In certain embodiments, at least one of the end groups is 5-10 membered heteroaryl ring optionally substituted with one or more alkyl.
  • In some embodiments, AE is absent. In some embodiments, AE is NHCO-.
  • In some embodiments, the first terminus comprises at least one C3-5 achiral aliphatic or heteroaliphatic amino acid.
  • In some embodiments, the first terminus comprises one or more subunits selected from the group consisting of optionally substituted pyrrole, optionally substituted imidazole, optionally substituted thiophene, optionally substituted furan, optionally substituted beta-alanine, γ-aminobutyric acid, (2-aminoethoxy)-propanoic acid, 3((2-aminoethyl)(2-oxo-2-phenyl-1λ2-ethyl)amino)-propanoic acid, or dimethylaminopropylamide monomer.
  • In some embodiments, the first terminus comprises a polyamide having the structure of Formula (A-6):
    Figure imgb0103
     wherein:
    • each A1 is NH- or -NH-(CH2)m-CH2-C(O)-NH-;
    • each M is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or optionally substituted alkylene;
    • m is an integer between 1 to 10; and
    • n is an integer between 1 and 6.
  • In some embodiments, each M1 in [A1-M1] of Formula (A-6) is a C6-10 arylene group, 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or C1-6 alkylene; each optionally substituted by 1-3 substituents selected from H, OH, halogen, C1-10 alkyl, NO2, CN, NR'R", C1-6 haloalkyl, - C1-6 alkoxyl, C1-6 haloalkoxy, (C1-6 alkoxy)C1-6 alkyl, C2-10alkenyl, C2-10alkynyl, C3-7 carbocyclyl, 4-10 membered heterocyclyl4-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, -(C3-7carbocyclyl)C1-6alkyl, (4-10 membered heterocyclyl4-10 membered heterocyclyl)C1-6alkyl, (C6-10aryl)C1-6alkyl, (C6-10aryl)C1-6alkoxy, (5-10 membered heteroaryl)C1-6alkyl, -(C3-7carbocyclyl)-amine, (4-10 membered heterocyclyl)amine, (C6-10aryl)amine, (5-10 membered heteroaryl)amine, acyl, C-carboxy, O-carboxy, C-amido, N-amido, S-sulfonamido, N-sulfonamido, -SR', COOH, or CONR'R"; wherein each R' and R" are independently H, C1-10alkyl, C1-10haloalkyl, -C1.10alkoxyl. In some embodiments, each R1 in [A1-R1] of Formula (A-6) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N or a C1-6 alkylene, and the heteroarylene or the a C1-6 alkylene is optionally substituted with 1-3 substituents selected from OH, halogen, C1-10 alkyl, NO2, CN, NR'R", C1-6 haloalkyl, -C1-6 alkoxyl, C1-6 haloalkoxy, C3-7 carbocyclyl, 4-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, -SR, COOH, or CONRR"; wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl. In some embodiments, each R1 in [A1-R1] of Formula (A-6) is a 5-10 membered heteroarylene containing at least one heteroatoms selected from O, S, and N, and the heteroarylene is optionally substituted with 1-3 substituents selected from OH, C1-6 alkyl, halogen, and C1-6 alkoxyl.
  • In some embodiments, the first terminus has a structure of Formula (A-7):
    Figure imgb0104
     or a salt thereof, wherein:
    • E is an end subunit which comprises a moiety chosen from a heterocyclic group or a straight chain aliphatic group, which is chemically linked to its single neighbor;
    • X1, Y1, and Z1 in each m' unit are independently selected from CR4, N, NR5, O, or S;
    • X2, Y2, and Z2 in each m3 unit are independently selected from CR4, N, NR5, O, or S;
    • X3, Y3, and Z3 in each m5 unit are independently selected from CR4, N, NR5, O, or S;
    • X4, Y4, and Z4 in each m7 unit are independently selected from CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl or C1-6alkylamine;
    • each m1, m3, m5 and m7 are independently an integer between 0 and 5;
    • each m2, m4 and m6 are independently an integer between 0 and 3; and m1 + m2 + m3+ m4+ m5+ m6+ m7 is between 3 and 15.
  • In some embodiments, m1 is 3, and X1, Y1, and Z1 in the first unit is respectively CH, N(CH3), and CH; X1, Y1, and Z1 in the second unit is respectively CH, N(CH3), and N; and X1, Y1, and Z1 in the third unit is respectively CH, N(CH3), and N. In some embodiments, m3 is 1, and X2, Y2, and Z2 in the first unit is respectively CH, N(CH3), and CH. In some embodiments, m5 is 2, and X3, Y3, and Z3 in the first unit is respectively CH, N(CH3), and N; X3, Y3, and Z3 in the second unit is respectively CH, N(CH3), and N. In some embodiments, m7 is 2, and X4, Y4, and Z4 in the first unit is respectively CH, N(CH3), and CH; X4, Y4, and Z4 in the second unit is respectively CH, N(CH3), and CH. In some embodiments, each m2, m4 and m6 are independently 0 or 1. In some embodiments, each of the X1, Y1, and Z1 in each m1 unit are independently selected from CH, N, or N(CH3). In some embodiments, each of the X2, Y2, and Z2 in each m3 unit are independently selected from CH, N, or N(CH3). In some embodiments, each of the X3, Y3, and Z3 in each m5 unit are independently selected from CH, N, or N(CH3). In some embodiments, each of the X4, Y4, and Z4 in each m7 unit are independently selected from CH, N, or N(CH3). In some embodiments, each Z1 in each m1 unit is independently selected from CR4 or NR5. In some embodiments, each Z2 in each m3 unit is independently selected from CR4 or NR5. In some embodiments, each Z3 in each m5 unit is independently selected from CR4 or NR5. In some embodiments, each Z4 in each m7 unit is independently selected from CR4 or NR5. In some embodiments, R4 is H, CH3, or OH. In some embodiments, R5 is H or CH3.
  • In some embodiments, for Formula (A-7), the sum of m2, m4 and m6 is between 1 and 6. In some embodiments, for formula (A-7), the sum of m2, m4 and m6 is between 2 and 6. In some embodiments, for Formula (A-7), the sum of m1, m3, m5 and m7 is between 2 and 10. In some embodiments, the sum of m1, m3, m5 and m7 is between 3 and 8. In some embodiments, for Formula (A-7), (m1 + m2 + m3+ m4+ m5+ m6+ m7) is between 3 and 12. In some embodiments, (m1 + m2 + m3+ m4+ m5+ m6+ m7) is between 4 and 10.
  • In some embodiments, for Formula (A-1) to (A-7), the first terminus comprises at least one beta-alanine moiety. In some embodiments, for Formula (A-1) to (A-7), the first terminus comprises at least two beta-alanine moieties. In some embodiments, for Formula (A-1) to (A-7), the first terminus comprises at least three or four beta-alanine moieties.
  • In some embodiments, the first terminus has the structure of Formula (A-8):
    Figure imgb0105
     or a salt thereof, wherein:
    • E is an end subunit which comprises a moiety chosen from a heterocyclic group or a straight chain aliphatic group, which is chemically linked to its single neighbor;
    • W is C1-6 alkylene,
      Figure imgb0106
    • X1', Y1, and Z1' in each n1 unit are independently selected from CR4, N, NR5, O, or S;
    • X2', Y2', and Z2' in each n3 unit are independently selected from CR4, N, NR5, O, or S;
    • X3', Y3', and Z3' in each n5 unit are independently selected from CR4, N, NR5, O, or S;
    • X4', Y4', and Z4' in each n6 unit are independently selected from CR4, N, NR5, O, or S;
    • X5', Y5', and Z5' in each n8 unit are independently selected from CR4, N, NR5, O, or S;
    • X6', y6', and Z6' in each n10 unit are independently selected from CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl or C1-6alkylaminen is an integer between 1 and 5;
    • each n1, n3, n5, n6, n8 and n10are independently an integer between 0 and 5;
    • each n2, n4, n7 and n9 are independently an integer between 0 and 3, and
    • n1 + n2 + n3+ n4+ n5+ n6+ n7+ n8+ n9+ n10 is between 3 and 15.
  • In some embodiments, for Formula (A-8), the sum of n2, n4, n7 and n9 is between 1 and 6. In some embodiments, for Formula (A-8), the sum of n2, n4, n7 and n9 is between 2 and 6. In some embodiments, for Formula (A-8), the sum of n1, n3, n5, n6, n8 and n10 is between 3 and 13. In some embodiments, the sum of n1, n3, n5, n6, n8 and n10 is between 4 and 10. In some embodiments, for Formula (A-8), (n1 + n2 + n3+ n4+ n5+ n6+ n7+ n8+ n9+ n10) is between 3 and 12. In some embodiments, (n1 + n2 + n3+ n4+ n5+ n6+ n7+ n8+ n9+ n10) is between 4 and 10.
  • In some embodiments, n1 is 3, and X1', Y1', and Z1' in the first unit is respectively CH, N(CH3), and CH; X1', Y1', and Z1' in the second unit is respectively CH, N(CH3), and N; and X1', Y1', and Z1' in the third unit is respectively CH, N(CH3), and N. In some embodiments, n3 is 1, and X2', Y2', and Z2' in the first unit is respectively CH, N(CH3), and CH. In some embodiments, n5 is 2, and X3', Y3', and Z3' in the first unit is respectively CH, N(CH3), and N; X3', Y3', and Z3' in the second unit is respectively CH, N(CH3), and N. In some embodiments, n6 is 2, and X4', Y4', and Z4' in the first unit is respectively CH, N(CH3), and N; X4', Y4', and Z4' in the second unit is respectively CH, N(CH3), and N. In some embodiments, the X1', Y1', and Z1' in each n1 unit are independently selected from CH, N, or N(CH3). In some embodiments, the X2', Y2', and Z2' in each n3 unit are independently selected from CH, N, or N(CH3). In some embodiments, the X3', Y3', and Z3' in each n5 unit are independently selected from CH, N, or N(CH3). In some embodiments, the X4', Y4', and Z4' in each n6 unit are independently selected from CH, N, or N(CH3). In some embodiments, the X5', Y3, and Z5' in each n8 unit are independently selected from CH, N, or N(CH3). In some embodiments, the X6', Y6', and Z6' in each n10 unit are independently selected from CH, N, or N(CH3). In some embodiments, each Z1' in each n1 unit is independently selected from CR4 or NR5. In some embodiments, each Z2' in each n3 unit is independently selected from CR4 or NR5. In some embodiments, each Z3' in each n5 unit is independently selected from CR4 or NR5. In some embodiments, each Z4' in each n6 unit is independently selected from CR4or NR5. In some embodiments, each Z5' in each n8 unit is independently selected from CR4 or NR5. In some embodiments, each Z6' in each n10 unit is independently selected from CR4 or NR5. In some embodiments, R4 is H, CH3, or OH. In some embodiments, R3 is H or CH3.
  • In some embodiments, the first terminus has the structure of Formula (A-9):
    Figure imgb0107
     or a salt thereof, wherein:
    • X1', Y1, and Z1' in each n1 unit are independently selected from CR4, N, NR5, O, or S;
    • X2', Y2', and Z2' in each n3 unit are independently selected from CR4, N, NR5, O, or S;
    • X3', Y3', and Z3' are independently selected from CR4, N, NR5, O, or S;
    • X4', Y4', and Z4' in each n6 unit are independently selected from CR4, N, NR5, O, or S;
    • X5', Y5', and Z5' in each n8 unit are independently selected from CR4, N, NR3, O, or S;
    • X6', Y6', and Z6' in each n9 unit are independently selected from CR4, N, NR5, O, or S;
    • X7', Y7', and Z7' in each n11 unit are independently selected from CR4, N, NR5, O, or S;
    • X8', Y8', and Z8' are independently selected from CR4, N, NR5, O, or S;
    • X9', Y9', and Z9' in each n14 unit are independently selected from CR4, N, NR5, O, or S;
    • X10', Y10', and Z10' in each n16 unit are independently selected from CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl or C1-6alkylamine;
    • each n1, n3, n6, n8, n9, n11, n14, and n16 are independently an integer between 0 and 5;
    • each n2, n4, n5, n7, n10, n13, and n15 are independently an integer between 0 and 3,
    • n1 + n2 + n3+ n4+ n5+ n6+ n7+ n8+ n9+ n10+n11+ n12+n13+n14+n15+ n16 is between 3 and 18 or a salt thereof, wherein:
      • L. is selected from a divalent or trivalent group selected from the group consisting of
        Figure imgb0108
         a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
        Figure imgb0109
      • each R1a and R1b are independently H, or an C1-6 alkyl;
      • each m and n are independently an integer between 1 and 10;
      • when La is a trivalent group, the oligomeric backbone is attached to the first terminus through La, and each E1a, E2a, E1b, and E2b are end groups independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, and optionally substituted amine;
      • when La is a divalent group, the oligomeric backbone is attached to the first terminus through one of E1a, E2a, E1b, and E2b, and each E1a E2a, E1b, and E2b are independently selected from the group consisting of a bond, a -C1-6 alkylene-, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, -C(O)-, -C(O)-C1-10alkylene, and - O-C0-6 alkylene, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, and optionally substituted amine; or
      • when L, is a bivalent group, the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of five-membered heteroaryl rings, and each E1a, E2a, E1b, and E2b are end groups independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, and optionally substituted amine.
  • In some embodiments, the first terminus comprises a polyamide having the structure of Formula (A-10):
    Figure imgb0110
     wherein:
    • each Y1, Y2, Z1, and Z2 are independently CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, or C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl, or C1-6 alkylamine ;
    • each W1 and W2 are independently a bond, NH, a C1-6 alkylene, -NH-C1-6 alkylene, -NH-5-10 membered heteroarylene, -NH-5-10 membered heterocyclene, -N(CH3)-C0-6 alkylene, -C(O)-, - C(O)-C1-10alkylene, or -O-C0-6 alkylene; and
    • n is an integer between 2 and 11.
  • In some embodiments, each R4 is independently H, -OH, halogen, C1-6 alkyl, C1-6 alkoxyl; and each R2 is independently H, C1-6 alkyl or C1-6alkylamine. In some embodiments, each R4 is selected from the group consisting of H, COH, Cl, NO, N-acetyl, benzyl, C1-6 alkyl, C1-6 alkoxyl, C1-6 alkenyl, C1-6 alkynyl, C1-6 alkylamine, -C(O)NH-(CH2)1-4-C(O)NH -(CH2)1-4-NRaRb; and each Ra and Rb are independently hydrogen or C1-6 alkyl.
  • In dome embodiments, R5 is independently selected from the group consisting of H, C1-6 alkyl, and C1-6 alkylNH2, preferably H, methyl, or isopropyl.
  • In some embodiments, R4 in Formula (A-7) to (A-8) is independently selected from H, OH, C1-6 alkyl, halogen, and C1-6 alkoxyl. In some embodiments, R4 in Formula (A-7) to (A-8) is selected from H, OH, halogen, C1-10 alkyl, NO2, CN, NR'R", C1-6 haloalkyl, -C1-6 alkoxyl, C1-6 haloalkoxy, (C1-6 alkoxy)C1-6 alkyl, C2-10alkenyl, C2-10alkynyl, C3-7 carbocyclyl, 4-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, -(C3-7carbocyclyl)C1-6alkyl, (4-10 membered heterocyclyl)C1-6alkyl, (C6-10aryl)C1-6alkyl, (C6-10aryl)C1-6alkoxy, (5-10 membered heteroaryl)C1-6alkyl, -(C3-7carbocyclyl)-amine, (4-10 membered heterocyclyl)amine, (C6-10aryl)amine, (5-10 membered heteroaryl)amine, acyl, C-carboxy, O-carboxy, C-amido, N-amido, S-sulfonamido, N-sulfonamido, -SR', COOH, or CONR'R"; wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl. In some embodiments, In some embodiments, R4 in Formula (A-7) to (A-8) is selected from O, S, and N or a C1-6 alkylene, and the heteroarylene or the a C1-6 alkylene is optionally substituted with 1-3 substituents selected from OH, halogen, C1-10 alkyl, NO2, CN, NR'R", C1-6 haloalkyl, -C1-6 alkoxyl, C1-6 haloalkoxy, C3-7 carbocyclyl, 4-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, -SR, COOH, or CONR'R"; wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl.
  • For the chemical Formula (A-1) to (A-9), each E, E1 and E2 independently are optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted immidazole containing moiety, and optionally substituted amine. In some embodiments, each E, E1 and E2 are independently selected from the group consisting of N-methylpyrrole, N-methylimidazole, benzimidazole moiety, and 3-(dimethylamino)propanamidyl, each group optionally substituted by 1-3 substituents selected from the group consisting of H, OH, halogen, C1-10 alkyl, NO2, CN, NR'R", C1-6 haloalkyl, -C1-6 alkoxyl, C1-6 haloalkoxy, (C1-6 alkoxy)C1-6 alkyl, C2-10alkenyl, C2-10alkynyl, C3-7 carbocyclyl, 4-10 membered heterocyclyl, C6-10aryl, 5-10 membered heteroaryl, amine, acyl, C-carboxy, O-carboxy, C-amido, N-amido, S-sulfonamido, N-sulfonamido, -SR, COOH, or CONRR"; wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl. In some embodiments, each E1 and E2 independently comprises thiophene, benzthiophene, C-C linked benzimidazole/thiophene-containing moiety, or C-C linked hydroxybenzimidazole/thiophene-containing moiety, wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl..
  • In some embodiments, each E, E1 or E2 are independently selected from the group consisting of isophthalic acid; phthalic acid; terephthalic acid; morpholine; N,N-dimethylbenzamide; N,N-bis(trifluoromethyl)benzamide; fluorobenzene; (trifluoromethyl)benzene; nitrobenzene; phenyl acetate; phenyl 2,2,2-trifluoroacetate; phenyl dihydrogen phosphate; 2H-pyran; 2H-thiopyran; benzoic acid; isonicotinic acid; and nicotinic acid; wherein one, two or three ring members in any of these end-group candidates can be independently substituted with C, N, S or O; and where any one, two, three, four or five of the hydrogens bound to the ring can be substituted with R5, wherein R5 may be independently selected for any substitution from H, OH, halogen, C1-10 alkyl, NO2, NH2, C1-10 haloalkyl, -OC1-10 haloalkyl, COOH, CONR'R"; wherein each R' and R" are independently H, C1-10 alkyl, C1-10 haloalkyl, -C1-10 alkoxyl.
  • The DNA recognition or binding moiety can include one or more subunits selected from the group consisting of:
    Figure imgb0111
    Figure imgb0112
    Figure imgb0113
    Figure imgb0114
    Figure imgb0115
    Figure imgb0116
    Figure imgb0117
     -NH-benzopyrazinylene-CO-, -NH-phenylene-CO-, -NH-pyridinylene-CO-, -NH-piperidinylene-CO-, -NH-pyrimidinylene-CO-, -NH-anthracenylene-CO-, -NH-quinolinylene-CO-, and
    Figure imgb0118
     wherein Z is H, NH2, C1-6 alkyl, or C1-6 alkylNH2.
  • In some sombodiments, Py is
    Figure imgb0119
     Im is
    Figure imgb0120
     Hp is
    Figure imgb0121
     Th is
    Figure imgb0122
     Pz is
    Figure imgb0123
     Nt is
    Figure imgb0124
     Tn is
    Figure imgb0125
     Nh is
    Figure imgb0126
     iNt is
    Figure imgb0127
     iIm is
    Figure imgb0128
     HpBi is
    Figure imgb0129
     ImBi is
    Figure imgb0130
     PyBi is
    Figure imgb0131
     Dp is
    Figure imgb0132
     -NH-benzopyrazinylene-CO- is
    Figure imgb0133
     -NH-phenylene-CO- is
    Figure imgb0134
     -NH-pyridinylene-CO- is
    Figure imgb0135
     -NH-piperidinylene-CO- is
    Figure imgb0136
     ,-NH-pyrazinylene-CO- is
    Figure imgb0137
     -NH-anthracenylene-CO- is
    Figure imgb0138
     and -NH-quinolinylene-CO- is
    Figure imgb0139
  • In some embodiments, the first terminus comprises one or more subunits selected from the group consisting of optionally substituted N-methylpyrrole, optionally substituted N-methylimidazole, and β-alanine (β).
  • In some embodiments, the first terminus does not have a structure of
    Figure imgb0140
  • The first terminus in the molecules described herein has a high binding affinity to a sequence having multiple repeats of GAA and binds to the target nucleotide repeats preferentially over other nucleotide repeats or nucleotide sequences. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CGG. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CCG. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CCTG. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of TGGAA. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of GGGGCC. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CAG. In some embodiments, the first terminus has a higher binding affinity to a sequence having multiple repeats of GAA than to a sequence having repeats of CTG.
  • Due to the preferential binding between the first terminus and the target nucleotide repeat, the transcription modulation molecules described herein become localized around regions having multiple repeats of GAA. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CGG. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CCG. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CCTG. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of TGGAA. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of GGGGCC. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CTG. In some embodiments, the local concentration of the first terminus or the molecules described herein is higher near a sequence having multiple repeats of GAA than near a sequence having repeats of CAG.
  • The first terminus is localized to a sequence having multiple repeats of GAA and binds to the target nucleotide repeats preferentially over other nucleotide repeats. In some embodiments, the sequence has at least 2, 3, 4, 5, 8, 10, 12, 15, 20, 25, 30, 40, 50, 100, 200, 300, 400, or 500 repeats of GAA. In certain embodiments, the sequence comprises at least 1000 nucleotide repeats of GAA. In certain embodiments, the sequence comprises at least 500 nucleotide repeats of GAA. In certain embodiments, the sequence comprises at least 200 nucleotide repeats of GAA. In certain embodiments, the sequence comprises at least 100 nucleotide repeats of GAA. In certain embodiments, the sequence comprises at least 50 nucleotide repeats of GAA. In certain embodiments, the sequence comprises at least 20 nucleotide repeats of GAA.
  • In one aspect, the compounds of the present disclosure can bind to the repeated GAA of fxn than to GAA elsewhere in the subject's DNA.
  • The polyamide composed of a pre-selected combination of subunits can selectively bind to the DNA in the minor groove. In their hairpin structure, antiparallel side-by-side pairings of two aromatic amino acids bind to DNA sequences, with a polyamide ring packed specifically against each DNA base. N-Methylpyrrole (Py) favors T, A, and C bases, excluding G; N-methylimidazole (Im) is a G-reader; and 3-hydroxyl-N-methylpyrrol (Hp) is specific for thymine base. The nucleotide base pairs can be recognized using different pairings of the amino acid subunits using the paring principle shown in Table 1A and 1B below. For example, an Im/Py pairing reads GC by symmetry, a Py/Im pairing reads C·G, an Hp/Py pairing can distinguish T·A from A·T, G·C, and C·G, and a Py/Py pairing nonspecifically discriminates both A·T and T.A from G·C and C·G.
  • In some embodiments, the first terminus comprises Im corresponding to the nucleotide G; Py or beta corresponding to the nucleotide A; Py corresponding to the nucleotide A, wherein Im is N-alkyl imidazole, Py is N-alkyl pyrrole, and beta is β-alanine. In some embodiments, the first terminus comprises Im/Py to correspond to the nucleotide pair G/C, Py/beta or Py/Py to correspond to the nucleotide pair A/T, and wherein Im is N-alkyl imidazole (e.g, N-methyl imidazole), Py is N-alkyl pyrrole (e.g., N-methyl pyrrole), and beta is β-alanine. Table 1A. Base paring for single amino acid subunit (Favored (+), disfavored (-))
    Subunit G C A T
    Py - + + +
    Im + - -
    Figure imgb0141
         		- - - +
    Figure imgb0142
         		- - + +
    Figure imgb0143
         		- - + +
    Figure imgb0144
         		- - + +
    Figure imgb0145
         		+ - - -
    Figure imgb0146
         		- - - +
    Figure imgb0147
         		+ - - -
    Figure imgb0148
         		- - - +
    Figure imgb0149
         		- + + +
    Figure imgb0150
         		+ - - -
    Figure imgb0151
         		+ - - -
    Figure imgb0152
         		- - - +
    Figure imgb0153
         		- - - +
    Figure imgb0154
    Figure imgb0155
         		- - + +
    Figure imgb0156
         		- - + (as a part of the turn) + (as a part of the turn)
    Figure imgb0157
         		- + - -
    Figure imgb0158
         		- - + +
    Figure imgb0159
         		- - + +
    Figure imgb0160
         		- - + +
    Figure imgb0161
         		+ + - -
    Figure imgb0162
         		- - + +
    Figure imgb0163
         		- - + +
    Figure imgb0164
         		WW* (bind to two nucleotides with same selectivity as Hp-Py)
    Figure imgb0165
         		WW* (bind to two nucleotides with same selectivity as Py-Py)
    Figure imgb0166
         		GW* (bind to two nucleotides with same selectivity as Im-Py)
    ∗The subunit HpBi, ImBi, and PyBi function as a conjugate of two monomer subunits and bind to two nucleotides. The binding property of HpBi, ImBi, and PyBi corresponds to Hp-Py, Im-Py, and Py-Py respectively.
    Table 1B. Base paring for hairpin polyamide
    G·C C·G T·A A·T
    Im/β + - - -
    β/Im - + - -
    Py/ β - - + +
    β/Py - - + +
    β/ β - - + +
    Py/Py - - + +
    Im/Im - - - -
    Im/Py + - - -
    Py/Im - + - -
    Th/Py - - + -
    Py/Th - - - +
    Th/Im + - - -
    Im/Th - + - -
    β/Th - - + -
    Th/β - - - +
    Hp/Py, - - + -
    Py/Hp, - - - +
    Hp/Im + - - -
    Im/Hp - + - -
    Tn/Py - - + +
    Py/Tn, - - + +
    Ht/Py, - - + +
    Py/Ht, - - + +
    Bi/Py, - - + +
    Py/Bi, - - + +
    β/Bi - - + +
    Bi/β - - + +
    Bi/Im, - + - -
    Im/Bi, + - - -
    Tp/Py, - - + +
    Py/Tp, - - + +
    β/Tp - - + +
    Tp/β - - + +
    Tp/Im, - + - -
    Im/Tp + - - -
    Tp/Tp - - + +
    Tp/Tn - - + +
    Tn/Tp - - + +
    Hz/Py, - - + -
    Py/Hz, - - - +
    Ip/Py + - - -
    Py/Ip, - + - -
    Bi/Hz, - - + +
    Hz/Bi, - - + +
    Bi/Bi - + + +
    Th/Py, - - + +
    Py/Th - - + +
    Im/gAB + - - -
    gAB/Im - + - -
    Py/ gAB + - - -
    gAB/Py - + - -
    gAB/ β - - + +
    β/gAB - - + +
    Im/Dp + - - -
    Dp/Im - + - -
    Py/ Dp - - + +
    Dp/Py - - + +
    Dp/β - - + +
    Each of HpBi, ImBi, and PyBi can bind to two nucleotides and have binding properties corresponding to Hp-Py, Im-Py, and Py-Py respectively. HpBi, ImBi, and PyBi can be paired with two monomer subunits or with themselves in a hairpin structure to bind to two nucleotide pairs.
  • The monomer subunits of the polyamide can be strung together based on the paring principles shown in Table 1A and Table 1B. The monomer subunits of the polyamide can be strung together based on the paring principles shown in Table 1C and Table 1D.
  • Table 1C shows an example of the monomer subunits that can bind to the specific nucleotide. The first terminus can include a polyamide described having several monomer subunits stung together, with a monomer subunit selected from each row. For example, the polyamide can include Im- β-Py that binds to GAA, with Im selected from the first G column, β from the A column, and Py from the second A column. The polyamide can be any combinations that bind to the subunits of GAA, with a subunit selected from each column in Table 1C, wherein the subunits are strung together following the GAA order.
  • In addition, the polyamide can also include a partial or multiple sets of the five subunits, such as 1.5, 2, 2.5, 3, 3.5, or 4 sets of the three subunits. The polyamide can include 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, and 16 monomer subunits. The multiple sets can be joined together by W. In addition to the five subunits or ten subunits, the polyamide can also include 1-4 additional subunits that can link multiple sets of the five subunits.
  • The polyamide can include monomer subunits that bind to 2, 3, 4, or 5 nucleotides of GAA. For example, the polyamide can bind to GA, AA, GAA, AAG, AGA, GAAG, AAGA, GAAGA or GAAGAA. The polyamide can include monomer subunits that bind to 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides of GAA repeats. The nucleotides can be joined by W.
  • The monomer subunit, when positioned as a terminal unit, does not have an amine or a carboxylic acid group at the terminal. The amine or carboxylic acid group in the terminal is replaced by a hydrogen. For example, Py, when used as a terminal unit, is understood to have the structure of
    Figure imgb0167
     (e.g,
    Figure imgb0168
     ); and Im, when positioned as a terminal unit, is understood to have the structure of
    Figure imgb0169
     (e.g,
    Figure imgb0170
     ). In addition, when Py or Im is used as a terminal unit, Py and Im can be respectively replaced by PyT
    Figure imgb0171
     (e.g.,
    Figure imgb0172
     ) and ImT
    Figure imgb0173
     (e.g.,
    Figure imgb0174
     ).
  • The linear polyamide can have nonlimiting examples including but not limited β-Py-Im, Im-Py-β-Im-Py-β-Im-Py, Im-Py-β-Im-Py-Py-lm-β, Im-Py-Py-Im-Py-β-Im-β, and any combinations thereof. Table 1C. Examples of monomer subunits in a linear polyamide that binds to GAA.
    Nucleotide G A A
    Subunit that selectively binds to nucleotide Im or ImT Py Py
    ilm or iImT Th Th
    PEG Pz Pz
    CTh Tp Tp
    Nt PEG PEG
    iPTA β β
    Ip iPP iPP
    CTh Da Da
    Dp Dp
    Dab Dab
    gAH gAH
  • The DNA-binding moiety can also include a hairpin polyamide having subunits that are strung together based on the pairing principle shown in Table 1B. Table 1D shows some examples of the monomer subunit pairs that selectively bind to the nucleotide pair. The hairpin polyamide can include 2n monomer subunits (n is an integer in the range of 2-8), and the polyamide also includes a W in the center of the 2n monomer subunits. W can be -(CH2)a-NR1-(CH2)b-, -(CH2)a-, -(CH2)a-O-(CH2)b-, -(CH2)a-CH(NHR1)-, - (CH2)
    Figure imgb0175
    -CH(NHR1)-, -(CR2R3)a -or -(CH2)a-CH(NR1 3)+-(CH2)b-, wherein each a is independently an integer between 2 and 4; R1 is H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, an optionally substituted C6-10 aryl, an optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; each R2 and R3 are independently H, halogen, OH, NHAc, or C1-4 alky. In some embodiments, W is -(CH2)-CH(NH3)+-(CH2)- or -(CH2)-CH2CH(NH3)+-. In some embodiments, R1 is H. In some embodiments, R1 is C1-6 alkyl optionally substituted by 1-3 substituents selected from -C(O)-phenyl. In some embodiments, W is -(CR2R3)-(CH2)a- or -(CH2)a-(CR2R3)-(CH2)b-, wherein each a is independently 1-3, b is 0-3, and each R2 and R3 are independently H, halogen, OH, NHAc, or C1-4 alky. W can be an aliphatic amino acid residue shown in Table 4 such as gAB.
  • When n is 2, the polyamide includes 4 monomer subunits, and the polyamide also includes a W joining the first set of two subunits with the second set of two subunits, Q1-Q2-W-Q3-Q4, and Q1/Q4 correspond to a first nucleotide pair on the DNA double strand, Q2/Q3 correspond to a second nucleotide pair, and the first and the second nucleotide pair is a part of the GAA repeat. When n is 3, the polyamide includes 6 monomer subunits, and the polyamide also includes a W joining the first set of three subunits with the second set of three subunits, Q1-Q2-Q3-W-Q4-Q5-Q6, and Q1/Q6 correspond to a first nucleotide pair on the DNA double strand, Q2/Q5 correspond to a second nucleotide pair, Q3/Q4 correspond to a third nucleotide pair, and the first and the second nucleotide pair is a part of the A repeat. When n is 4, the polyamide includes 8 monomer subunits, and the polyamide also includes a W joining the first set of four subunits with the second set of four subunits, Q1-Q2-Q3-Q4-W-Q5-Q6-Q7-Q8, and Q1/Q8 correspond to a first nucleotide pair on the DNA double strand, Q2/Q7 correspond to a second nucleotide pair, Q3/Q6 correspond to a third nucleotide pair, and Q4/Q5 correspond to a fourth nucleotide pair on the DNA double strand. When n is 5, the polyamide includes 10 monomer subunits, and the polyamide also includes a W joining a first set of five subunits with a second set of five subunits, Q1-Q2-Q3-Q4-Q5-W-Q6-Q7-Q8-Q9-Q10, and Q1/Q10, Q2/Q9, Q3/Q8, Q4/Q7, Q5/Q6 respectively correspond to the first to the fifth nucleotide pair on the DNA double strand. When n is 6, the polyamide includes 12 monomer subunits, and the polyamide also includes a W joining a first set of six subunits with a second set of six subunits, Q1-Q2-Q3-Q4-Q5-Q6-W-Q7-Q8-Q9-Q10-Q11-Q12, and Q1/Q12, Q2/Q11, Q3/Q10, Q4/Q9, Q5/Q8, Q6/Q7 respectively correspond to the first to the six nucleotide pair on the DNA double strand. When n is 8, the polyamide includes 16 monomer subunits, and the polyamide also includes a W joining a first set of eight subunits with a second set of eight subunits, Q1-Q2-Q3-Q4-Q5-Q6-Q7-Q8-W-Q9-Q10-Q11-Q12-Q13-Q14-Q15-Q16, and Q1/Q16, Q2/Q15, Q3/Q14, Q4/Q13, Q5/Q12, Q6/Q11, Q7/Q10, and Q8/Q9 respectively correspond to the first to the eight nucleotide pair on the DNA double strand. In some hairpin polyamide structures, the number of monomer subunits on each side of W can be different, and one side of the hairpin can partial pair with the other side of the hairpin to bind the nucleotide pairs on a double strand DNA based on the binding principle in Table 1B and 1D, while the rest of the unpaired monomer subunit(s) can bind to the nucleotide based on the binding principle in Table 1A and 1C but does not pair with the mononer subunit on the other side. The hairpin polyamide can have one or more overhanging monomer subunit that binds to the nucleotide but does not pair with the monomer subunit on the antiparrallel strandFor example, the hairpin structure can include 5 monomer subunits on one side of W and 4 monomer subunits on the other side of W, Q1-Q2-Q3-Q4-Q5-W-Q6-Q7-Q8-Q9, and Q2/Q9, Q3/Q8, Q4/Q7, Q5/Q6 respectively correspond to the first to the fourth nucleotide pair on the DNA double strand, and Q1 binds to a single nucleotide but does not pair with a monomer subunit on the other strand to bind with a nucleotide pair. W can be an aliphatic amino acid residue such as gAB or other appropriate spacers as shown in Table 4. In some instances, when W is gAB, it favors binding to T.
  • Because the target gene can include multiple repeats of GAA, the subunits can be strung together to bind at least two, three, four, five, six, seven, eight, nine, or ten nucleotides in one or more GAA repeat (e.g., GAAGAAGAAGAA). For example, the polyamide can bind to the GAA repeat by binding to a partial copy, a full copy, or a multiple repeats of GAA such as GA, AA, GAA, AAG, AGA, GAAG, AAGA, GAAGA or GAAGAA. For example, the polyamide can include Im-Py-β-W-Py-β-Py that binds to GAA and its complementary nucleotides on a double strand DNA, in which the Im/Py pair binds to the G·C, the Py/β pair binds to A·T, and the β/Py pair binds to G.A. In another example Im-Py-β-Im-W-β-Py-β-Py that binds to GAAG and its complementary nucleotides on a double strand DNA, in which the Im/Py pair binds to the G·C, the Py/β pair binds to A·T, the β/Py pair binds to G·A, and the Im/β pair binds to the G·C,. W can be an aliphatic amino acid residue such as gAB or other appropriate spacers as shown in Table 4. In another example, Im-Py-β-Im-gAB-Im-Py binds to with a part of the complementary nucletides (ACG) on the double strand DNA, in wihch Im binds to G, Py binds to A, β/Py binds to the A·T, Im/Im binds to G·C.
  • Some additional examples of the polyamide include but are not limited to Im-Py-Py-Im-gAB-Py-Im-Im-Py; Im-Py-Py-Im-gAB-Py-Im-Im-PyT; Im-Py-Py-Im-gAB-Py-Im-Im-β; Im-Py-Py-Im-gAB-Py-Im-Im-β-G; Im-β-Py-Im-gAB-Py-Im-Im-β; Im-β-Py-Im-gAB-Py-Im-Im-β-G; Im-β-Py-Im-gAB-Py-Im-Im-Py; Im-β-Py-Im-gAB-Py-Im-Im-PyT; Py-Py-Im-β-gAB-Im-Py-Im-Im; Py-Py-Im-β-gAB-Im-Py-Im-ImT; Py-Py-Im-Py-gAB-Im-Py-Im-Im; Py-Py-Im-Py-gAB-Im-Py-Im-ImT; Py-Py-Im-β-gAB-Im-β-Im-Im; Py-Py-Im-β-gAB-Im-β-Im-ImT; Py-Py-Im-Py-gAB-Im-β-Im-Im; Py-Py-Im-Py-gAB-Im-β-Im-ImT; Im-β-Py-gAB-Im-Im-Py; Im-β-Py-gAB-Im-Im-PyT; Im-β-Py-gAB-Im-Im-β; Im-β-Py-gAB-Im-Im-β-G; Im-Py-Py-gAB-Im-Im-β; Im-Py-Py-gAB-Im-Im-β-G; Im-Py-Py-gAB-Im-Im-Py; Im-Py-Py-gAB-Im-Im-PyT; Im-p-Py-gAB-Im-Im-Py; and Im-β-Py-gAB-Im-Im-PyT; wherein G may be hydrogen, alkyl, alkenyl, alkynyl, or - C(O)-RB; and RB may be a hydrogen, C1-C6 alkyl, C1-C6 alkenyl, or C1-C6 alkynyl group. In some embodiments, the hairpin polyamide has a structure of Im-Py-β-Im-gAB-Im-Py; Im-Py-β-Im-gAB-Im-Py-β-Im; Py-β-Im-gAB-Im-Py-β-Im; or β-Im-gAB-Im-Py-β-Im. Table 1D. Examples of monomer pairs in a hairpin or H-pin polyamide that binds to GAA.
    Nucleotide G·C A·T A·T
    Subunit pairs that selectively binds to nucleotide Im/β Py/ β Py/ β
    Im/Py β/Py β/Py
    Th/Im PIP PIP
    Hp/Im Py/Py Py/Py
    Im/Bi Py/Th Py/Th
    Im/Tp Th/β Th/β
    Ip/Py Py/Hp, Py/Hp,
    Im/gAB Tn/Py Tn/Py
    Py/gAB Py/Tn, Py/Tn,
    Im/Dp Ht/Py, Ht/Py,
    Py/Ht, Py/Ht,
    Bi/Py, Bi/Py,
    Py/Bi, Py/Bi,
    β/Bi β/Bi
    Bi/β Bi/β
    Tp/Py, Tp/Py,
    Py/Tp, Py/Tp,
    β/Tp β/Tp
    Tp/β Tp/β
    Tp/Tp Tp/Tp
    Tp/Tn Tp/Tn
    Tn/Tp Tn/Tp
    Py/Hz, Py/Hz,
    Bi/Hz, Bi/Hz,
    Hz/Bi, Hz/Bi,
    Bi/Bi Bi/Bi
    Th/Py, Th/Py,
    Py/Th Py/Th
    gAB/ β gAB/ β
    β/gAB β/gAB
    Pyl Dp Pyl Dp
    DpIPy Dp/Py
    Dp/β Dp/β
  • Recognition of a nucleotide repeat or DNA sequence by two antiparallel polyamide strands depends on a code of side-by-side aromatic amino acid pairs in the minor groove, usually oriented N to C with respect to the 5' to 3' direction of the DNA helix. Enhanced affinity and specificity of polyamide nucleotide binding is accomplished by covalently linking the antiparallel strands. The "hairpin motif" connects the N and C termini of the two strands with a W (e.g., gamma-aminobutyric acid unit (gamma-turn)) to form a folded linear chain. The "H-pin motif" connects the antiparallel strands across a central or near central ring/ring pairs by a short, flexible bridge.
  • The DNA-binding moiety can also include a H-pin polyamide having subunits that are strung together based on the pairing principles shown in Table 1A and/or Table 1B. Table 1C shows some examples of the monomer subunit that selectively binds to the nucleotide, and Table 1D shows some examples of the monomer subunit pairs that selectively bind to the nucleotide pair. The h-pin polyamide can include 2 strands and each strand can have a number of monomer subunits (each strand can include 2-8 monomer subunits), and the polyamide also includes a bridge L1 to connect the two strands in the center or near the center of each strand. At least one or two of the monomer subunits on each strand are paired with the corresponding monomer subunits on the other stand following the paring principle in Table 1D to favor binding of either GC or C·G, A·T, or T·A pair, and these monomer subunit pairs are often positioned in the center, close to center region, at or close to the bridge that connects the two strands. In some instances, the H-pin polyamide can have all of the monomer subunits be paired with the corresponding monomer subunits on the antiparallel strand based on the paring principle in Table 1B and 1D to bind to the nucleotide pairs on the double strand DNA. In some instances, the H-pin polyamide can have a part of the monomer subunits (2, 3, 4, 5, or 6) be paired with the corresponding monomer subunits on the antiparallel strand based on the binding principle in Table 1B and 1D to bind to the nucleotide pairs on the double strand DNA, while the rest of the monomer subunit binds to the nucleotide based on the binding principle in Table 1A and 1C but does not pair with the mononer subunit on the antiparallel strand. The h-pin polyamide can have one or more overhanging monomer subunit that binds to the nucleotide but does not pair with the nomoner subunit on the antiparrallel strand.
  • Another polyamide structure that derives from the h-pin structure is to connect the two antiparallel strands at the end through a bridge, while only the two mononer subunits that are connected by the bridge form a pair that bind to the nucleotide pair G·C or C.G based on the binding principle in Table 1B/1D, but the rest of the monomer subunits on the strand form an overhang, bind to the nucleotide based on the binding principle in Table 1A and/or 1C and do not pair with the monomer subunit on the other strand.
  • The bridge can be is a bivalent or trivalent group selected from
    Figure imgb0176
    Figure imgb0177
     a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
    Figure imgb0178
     -(CH2)a-NR1-(CH2)b-, - (CH2)a-, -(CH2)a-O-(CH2)b-, -(CH2)a-CH(NHR1)-, -(CH2)a-CH(NHR1)-, -(CR2R3)a- or -(CH2)a-CH(NR1 3)+-(CH2)b-, wherein m is an integer in the range of 0 to 10; n is an integer in the range of 0 to 10; each a is independently an integer between 2 and 4; R1 is H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, an optionally substituted C6-10 aryl, an optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; each R2 and R3 are independently H, halogen, OH, NHAc, or C1-4 alky. In some embodiments, W is -(CH2)-CH(NH3)+-(CH2)- or -(CH2)-CH2CH(NH3)+-. In some embodiments, R1 is H. In some embodiments, R1 is C1-6 alkyl optionally substituted by 1-3 substituents selected from -C(O)-phenyl. In some embodiments, L1 is -(CR2R3)-(CH2)a- or -(CH2)a-(CR2R3)-(CH2)b-, wherein each a is independently 1-3, b is 0-3, and each R2 and R3 are independently H, halogen, OH, NHAc, or C1-4 alky. L1 can be a C2-9 alkylene or (PEG)2-8.
  • When n is 3, the polyamide includes 6 monomer subunits, and the polyamide also includes a bridge L1 joining the first set of three subunits with the second set of three subunits, and Q1-Q2-Q3 can be joined to Q4-Q5-Q6 through L1 at the center Q2 and Q5, and Q1/Q4 correspond to a first nucleotide pair on the DNA double strand, Q2/Q5 correspond to a second nucleotide pair, Q3/Q6 correspond to a third nucleotide pair. When n is 4, the polyamide includes 8 monomer subunits, and the polyamide also includes a bridge L1 joining the first set of four subunits with the second set of four subunits, Q1-Q2-Q3-Q4 can be joined to Q5-Q6-Q7-Q8 through L1 at Q2 and Q6 Q2 and Q7, Q3 and Q6, or Q3 and Q7 positions; Q1/Q5 may correspond to a nucleotide pair on the DNA double strand, and Q3/Q8 may correspond to another nucleotide pair; or Q1 and Q8 form overhangs on each strand, or Q and Q5 form overhangs on each strand. When n is 5, the polyamide includes 10 monomer subunits, and the polyamide also includes a bridge L1 joining a first set of five subunits with a second set of five subunits, and Q1-Q2-Q3-Q4-Q5 can be joined to Q6-Q7-Q8-Q9-Q10 through a bridge L1 at non-terminal positions (any position except for Q1, Q5, Q6 and Q10); if the two strands are linked at Q3 and Q8 by the bridge, Q1/Q6, Q2/Q7, Q3/Q8, Q4/Q9, and Q5/Q10 can be paired to bind to the nucleotide pairs; if the two strands are linked at Q2 and Q9 by the bridge, then Q1/Q8, Q3/Q10 can be paired to bind to the nucleotide pairs, Q4 and Q5 form an overhang on one strand and Q6 and Q7 form an overhang on the other strand.
  • In some embodiments, the monomer subunit at the central or near the central (n/2, (n±1)/2) on one strand is paired with the corresponding one on the other strand to bind to the nucleotide pairs on the double stranded DNA. In some embodiments, the monomer subunit at the central or near the central (n/2, ( n±1)/2) on one strand is connected with the corresponding one on the other strand through a bridge L1.
  • When n is 4, the polyamide includes 8 monomer subunits, and the polyamide also includes a bridge L1 joining the first set of four subunits with the second set of four subunits, Q1-Q2-Q3-Q4 can be joined to Q5-Q6-Q7-Q8 at the end Q4 and Q5 through L1; while Q4/Q5 can be paired to bind to the nucleotide pairs, Q1-Q2-Q3 form an overhang on one strand and Q6-Q7-Q8 form an overhang on the other strand.
  • Some additional examples of the polyamide include but are not limited to Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py, Im-Py-Py-Im (Linked in the middle - position 3 py and Py) to Im-Py-β-Py-Py, Im-Py-β-Im (linked to the bolded position) Im-Py; Im-Py-β-Im (linked in the middle, either position 2 or 3) Im-Py-b-Im; Py-β-Im (linked to the middle position bolded) Im-Py-β-Im; or β-Im (linked at bolded position) Im-Py-β-Im.
    • Second Terminus -Regulatory protein binding moiety
  • In certain embodiments, the regulatory molecule is chosen from a nucleosome remodeling factor (NURF), a bromodomain PHD finger transcription factor (BPTF), a ten-eleven translocation enzyme (TET), methylcytosine dioxygenase (TET1), a DNA demethylase, a helicase, an acetyltransferase, and a histone deacetylase ("HDAC").
  • The binding affinity between the regulatory protein and the second terminus can be adjusted based on the composition of the molecule or type of protein. In some embodiments, the second terminus binds the regulatory molecule with an affinity of less than about 600 nM, about 500 nM, about 400 nM, about 300 nM, about 250 nM, about 200 nM, about 150 nM, about 100 nM, or about 50nM. In some embodiments, the second terminus binds the regulatory molecule with an affinity of less than about 300 nM. In some embodiments, the second terminus binds the regulatory molecule with an affinity of less than about 200 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity of greater than about 200 nM, about 150 nM, about 100 nM, about 50 nM, about 10 nM, or about 1 nM. In some embodiments, the polyamide is capable of binding the DNA with an affinity in the range of about 1-600 nM, 10-500 nM, 20-500 nM, 50-400 nM, 100-300 nM, or 50-200 nM.
  • In some embodiments, the second terminus comprises one or more optionally substituted C6-10 aryl, optionally substituted C4-10 carbocyclic, optionally substituted 4 to 10 membered heterocyclic, or optionally substituted 5 to 10 membered heteroaryl.
  • In some embodiments, the protein-binding moiety binds to the regulatory molecule that is selected from the group consisting of a CREB binding protein (CBP), a P300, an O-linked β-N-acetylglucosamine-transferase- (OGT-), a P300-CBP-associated-factor- (PCAF-), histone methyltransferase, histone demethylase, chromodomain, a cyclin-dependent-kinase-9- (CDK9-), a nucleosome-remodeling-factor-(NURF-), a bromodomain-PHD-finger-transcription-factor- (BPTF-), a ten-eleven-translocation-enzyme-(TET-), a methylcytosine-dioxygenase- (TET1-), histone acetyltransferase (HAT), a histone deacetalyse (HDAC), , a host-cell-factor-1(HCF1-), an octamer-binding-transcription-factor- (OCT1-), a P-TEFb-, a cyclin-T1-, a PRC2-, a DNA-demethylase, a helicase, an acetyltransferase, a histone-deacetylase, methylated histone lysine protein.
  • In some embodiments, the second terminus comprises a moiety that binds to an O-linked β-N-acetylglucosamine-transferase (OGT), or CREB binding protein (CBP). In some embodiments, the protein binding moiety is a residue of a compound that binds to an O-linked β-N-acetylglucosamine-transferase(OGT), or CREB binding protein (CBP).
  • In some embodiments, the second terminus does not comprises JQ1, iBET762, OTX015, RVX208, or AU1. In some embodiments, the second terminus does not comprises JQ1. In some embodiments, the second terminus does not comprises a moiety that binds to a bromodomain protein.
  • In some embodiments, the second terminus comprises a diazine or diazepine ring, wherein the diazine or diazepine ring is fused with a C6-10 aryl or a 5-10 membered heteroaryl ring comprising one or more heteroatom selected from S, N and O.
  • In some embodiments, the second terminus comprises an optionally substituted bicyclic or tricyclic structure. In some embodiments, the optionally substituted bicyclic or tricyclic structure comprises a diazepine ring fused with a thiophene ring.
  • In some embodiments, the second terminus does not comprise an optionally substituted bicyclic structure, wherein the bicyclic structure comprises a diazepine ring fused with a thiophene ring.
  • In some embodiments, the second terminus does not comprise an optionally substituted tricyclic structure, wherein the tricyclic structure is a diazephine ring that is fused with a thiophene and a triazole.
  • In some embodiments, the second terminus does not comprise an optionally substituted diazine ring.
  • In some embodiments, the second terminus does not comprise a structure of Formula (C-11):
    Figure imgb0179
     wherein:
    • each of A1p and B1p is independently an optionally substituted aryl or heteroaryl ring;
    • X1p is CH or N;
    • R1p is hydrogen, halogen, or an optionally substituted C1-6 alkyl group; and
    • R2p is an optionally substituted C1-6 alkyl, cycloalkyl, C6-10 aryl, or heteroaryl.
  • In some embodiments, X1p is N. In some embodiments, A1p is an aryl or heteroaryl substituted with one or more substituents. In some embodiments, A1p is an aryl or heteroaryl substituted with one or more substituents selected from halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, and C1-6haloalkyl. In some embodiments, B1p is an optionally substituted aryl or heteroaryl substituted with one or more substituents selected from halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, and C1-6haloalkyl.
  • In some embodiments, A1p is an optionally substituted thiophene or phenyl. In some embodiments, A1p is a thiophene or phenyl, each substituted with one or more substituents selected from halogen, C1-6 alkyl, hydroxyl, C1-6 alkoxy, and C1-6 haloalkyl. In some embodiments, B1p is an optionally substituted triazole. In some embodiments, B1p is a triazole substituted with one or more substituents selected from halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, and C1-6haloalkyl.
  • In some embodiments, the protein binding moiety is not
    Figure imgb0180
    Figure imgb0181
  • In some embodiments, the protein binding moiety is not
    Figure imgb0182
  • In some embodiments, the protein binding moiety does not have the structure of Formula (C-12):
    Figure imgb0183
     wherein:
    • R1q is a hydrogen or an optionally substituted alkyl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, halogenated alkyl, hydroxyl, alkoxy, or -COOR4q;
    • R4q is hydrogen, or an optionally substituted aryl, aralkyl, cycloalkyl, heteroaryl, heteroaralkyl, heterocycloalkyl, alkyl, alkenyl, alkynyl, or cycloalkylalkyl group, optionally containing one or more heteroatoms;
    • R2q is an optionally substituted aryl, alkyl, cycloalkyl, or aralkyl group;
    • R3q is hydrogen, halogen, or an optionally substituted alkyl group, preferably (CH2)x - C(O)N(R20)(R21), or (CH2)x-N(R20)-C(O)R21; or halogenated alkyl group;
    • wherein x is an integer from 1 to 10; and R20 and R21 are each independently hydrogen or C1-C6 alkyl group, preferably R20 is hydrogen and R21 ismethyl; and
    • Ring E is an optionally substituted aryl or heteroaryl group.
  • The protein binding moiety can include a residue of a compound that binds to a regulatory protein. In some embodiments, the protein binding moiety can be a residue of a compound shown in Table 2. Exemplary residues include, but are not limited to, amides, carboxylic acid esters, thioesters, primary amines, and secondary amines of any of the compounds shown in Table 2.
    Figure imgb0184
    Figure imgb0185
    Figure imgb0186
    Figure imgb0187
    Figure imgb0188
    Figure imgb0189
    Figure imgb0190
    Figure imgb0191
    Figure imgb0192
    Figure imgb0193
    Figure imgb0194
    Figure imgb0195
    Figure imgb0196
    Figure imgb0197
    Figure imgb0198
    Figure imgb0199
    Figure imgb0200
    Figure imgb0201
    Figure imgb0202
    Figure imgb0203
    Figure imgb0204
    Figure imgb0205
    Figure imgb0206
    Figure imgb0207
    Figure imgb0208
    Figure imgb0209
    Figure imgb0210
    Figure imgb0211
    Figure imgb0212
    Figure imgb0213
    Figure imgb0214
    Figure imgb0215
    Figure imgb0216
    Figure imgb0217
    Figure imgb0218
    Figure imgb0219
    Figure imgb0220
    Figure imgb0221
    Figure imgb0222
    Figure imgb0223
    Figure imgb0224
    Figure imgb0225
    Figure imgb0226
    Figure imgb0227
    Figure imgb0228
    Figure imgb0229
    Figure imgb0230
    Figure imgb0231
    Figure imgb0232
    Figure imgb0233
    Figure imgb0234
    Figure imgb0235
    Figure imgb0236
    Figure imgb0237
    Figure imgb0238
    Figure imgb0239
    Figure imgb0240
    Figure imgb0241
    Figure imgb0242
    Figure imgb0243
    Figure imgb0244
    Figure imgb0245
    Figure imgb0246
    Figure imgb0247
    Figure imgb0248
    Figure imgb0249
    Figure imgb0250
    Figure imgb0251
    Figure imgb0252
    Figure imgb0253
    Figure imgb0254
    Figure imgb0255
    Figure imgb0256
    Figure imgb0257
    Figure imgb0258
    Figure imgb0259
    Figure imgb0260
    Figure imgb0261
    Figure imgb0262
    Figure imgb0263
    Figure imgb0264
    Figure imgb0265
    Figure imgb0266
    Figure imgb0267
    Figure imgb0268
    Figure imgb0269
    Figure imgb0270
    Figure imgb0271
    Figure imgb0272
    Figure imgb0273
    Figure imgb0274
    Figure imgb0275
    Figure imgb0276
    Figure imgb0277
    Figure imgb0278
    Figure imgb0279
    Figure imgb0280
    Figure imgb0281
    Figure imgb0282
    Figure imgb0283
    Figure imgb0284
    Figure imgb0285
    Figure imgb0286
    Figure imgb0287
  • In some embodiments, the second terminus does not comprises JQ1, JQ-1, OTX015, RVX208 acid, or RVX208 hydroxyl.
  • In certain embodiments, the the protein binding moiety is a residue of a compound having a structure of Formula (C-1):
    Figure imgb0288
     wherein:
    • Xa is -NHC(O)-, -C(O)-NH-, -NHSO2-, or -SO2NH-;
    • Aa is selected from an optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl;
    • Xb is a bond, NH, NH-C1-10alkylene, -C1-12 alkyl, NHC(O)-, or -C(O)-NH-;
    • Ab is selected from an optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 4- to 10-membered heterocycloalkyl; and
    • each R1e, R2e, R3e, R4e are independently selected from the group consisting of H, OH, - NO2, halogen, amine, COOH, COOC1-10alkyl, NHC(O)-optionally substituted -C1-12 alkyl, - NHC(O)(CH2)1-4NRfRg, -NHC(O)(CH2)0-4 CHRf(NRfR'g), -NHC(O)(CH2)0-4 CHRfRg, - NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to 10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to 10-membered heteroaryl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 4- to 10-membered heterocycloalkyl, and
    • wherein each Rf and Rg are independently H or C1-6 alkyl.
  • In certain embodiments, the the protein binding moiety is a residue of a compound having a structure of Formula (C-2):
    Figure imgb0289
     wherein R5e is independently selected from the group consisting of H, COOC1-10alkyl, NHC(O)-optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkylsubstituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl.
  • In certain embodiments, Aa is selected from an optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5-to 10-membered heterocycloalkyl. In certain embodiments, Aa is an optionally substituted C6-10 aryl.
  • In certain embodiments, the the protein binding moiety is a residue of a compound having a structure of Formula (C-3):
    Figure imgb0290
     wherein:
    • M1c is CR2h or N; and
    • each R1h, R2h, R3h, R4h, and R5h are independently selected from the group consisting of H, OH, -NO2, halogen, amine, COOH, COOC1-10alkyl, NHC(O)-optionally substituted -C1-12 alkyl, - NHC(O)(CH2)1-4NRfRg, -NHC(O)(CH2)0-4 CHRf(NRfRg), -NHC(O)(CH2)0-4 CHRfRg, - NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to 10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to 10-membered heteroaryl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl, wherein each Rf and Rg are independently H or C1-6 alkyl.
  • In certain embodiments, each R1h and R5h are independently hydrogen, halogen, or C1-6 alkyl. In certain embodiments, each R2h and R3h are independently H, OH, -NO2, halogen, C1-4 haloalkyl, amine, COOH, COOC1-10alkyl, -NHC(O)-optionally substituted -C1-12 alkyl, -NHC(O)(CH2)1-4NRfRg, - NHC(O)(CH2)0-4 CHR'(NR'R"), -NHC(O)(CH2)0-4 CHRfRg, -NHC(O)(CH2)0-4-C3-7 cycloalkyl, - NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to 10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to 10-membered heteroaryl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl. In certain embodiments, R1e, R3e, and R4e are hydrogen.
  • In certain embodiments, R2e is selected from the group consisting of H, OH, -NO2, halogen, amine, COOH, COOC1-10alkyl, NHC(O)-optionally substituted -C1-12 alkyl, NHC(O)(CH2)1-4NRfRg, - NHC(O)(CH2)0-4 CHRf(NRfRg), -NHC(O)(CH2)0-4 CHRfRg, -NHC(O)(CH2)0-4-C3-7 cycloalkyl, - NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to 10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to 10-membered heteroaryl, optionally substituted -C1-12 alkyl, -optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5-to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl, wherein each Rf and Rg are independently H or C1-6 alkyl.
  • In certain embodiments, R2e is an phenyl or pyridinyl optionally substituted with 1-3 substituents, wherein the substituent is independently selected from the group consisting of OH, -NO2, halogen, amine, COOH, COOC1-10alkyl, NHC(O) -C1-12 alkyl, -NHC(O)(CH2)1-4NRfRg, -NHC(O)(CH2)0-4 CHRf (NRfRg), - NHC(O)(CH2)0-4 CHRfRg, -NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to 10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to 10-membered heteroaryl, -C1-12 alkoxyl, C1-12 haloalkyl, C6-10 aryl, C3-7 cycloalkyl, 5- to 10-membered heteroaryl, and 5- to 10-membered heterocycloalkyl, wherein each Rf and Rg are independently H or C1-6 alkyl
  • In certain embodiments, Aa is a C6-10 aryl substituted with 1-4 substituents, and each substituent is independently selected from halogen, OH, NO2, an optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl.
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-4):
    Figure imgb0291
     wherein:
    • R1c is an optionally substituted C6-10 aryl or an optionally substituted 5- to 10-membered heteroaryl,
    • Xc is -C(O)NH-, -C(O), -S(O2)-, -NH-, or -C1-4alkyl-NH,
    • n is 0-10,
    • R2j is -NR3jR4j, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, or optionally substituted 4- to 10-membered heterocycloalkyl; and
    • each R3j and R4j are independently H or optionally substituted -C1-12 alkyl.
  • ln some embodiments, R2j is -NHC(CH3)3, or a 4- to 10-membered heterocycloalkyl substituted with C1-12alkyl.
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-5):
    Figure imgb0292
     wherein:
    • X2c is a bond, C(O), SO2, or CHR3c;
    • M2c is CH or N;
    • n is 0-10,
    • R2j is -NR3jR4j, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, or optionally substituted 4- to 10-membered heterocycloalkyl;
    • each R5j is independently -NR3jR4j, -C(O)R3j, -COOH, -C(O)NHC1-6alkyl, an optionally substituted C6-10 aryl, or an optionally substituted 5- to 10-membered heteroaryl;
    • R6j is -NR3jR4j, -C(O)R3j, an optionally substituted C6-10 aryl, or an optionally substituted 5-to 10-membered heteroaryl; and
    • each R3j and R4j are independently H, an optionally substituted C6-10 aryl, optionally substituted 4- to 10-membered heterocycloalkyl, or optionally substituted -C1-12 alkyl.
  • In certain embodiments, R2j is a 4- to 10-membered heterocycloalkyl substituted by a 4- to 10-membered heterocycloalkyl. In certain embodiments, R6j is -C(O)R3j, and R3j is a 4- to 10-membered heterocycloalkyl substituted by a 4- to 10-membered heterocycloalkyl. In certain embodiments, each R5j is independently H, -C(O)R3j, -COOH, -C(O)NHC1-6alkyl, -NH-C6-10 aryl, or optionally substituted C6-10 aryl
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-6):
    Figure imgb0293
     wherein:
    • X3c is a bond, NH, C1-4 alkylene, or NC1-4 alkyl;
    • R7j is an optionally substituted C1-6 alkyl, an optionally substituted cyclic amine, an optionally substituted aryl, an optionally substituted 5- to 10-membered heteroaryl, or optionally substituted 4- to 10-membered heterocycloalkyl,
    • R8j is H, halogen, or C1-6 alkyl; and
    • R9j is H, or C1-6 alkyl.
  • In certain embodiments, R7j is an optionally substituted cyclic secondary or tertiary amine. In certain embodiments, R7j is a tetrahydroisoquinoline optionally substituted with C1-4 alkyl.
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-7):
    Figure imgb0294
     wherein:
    • A1a is an optionally substituted aryl or heteroaryl;
    • X2 is a bond, (CH2)1-4, or NH; and
    • A2a is an optionally substituted aryl, heterocyclic, or heteroaryl, linked to an amide group.
  • In certain embodiments, A1a is an aryl substituted with one or more halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, or C1-6haloalkyl. In certain embodiments, X2 is NH. In certain embodiments, A2a is a heterocyclic group. In certain embodiments, A2a is a pyrrolidine. In certain embodiments, A2a is an optionally substituted phenyl. In certain embodiments, A2a is a phenyl optionally substituted with one or more halogen, C1-6 alkyl, hydroxyl, C1-6 alkoxy, or C1-6 haloalkyl.
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-8):
    Figure imgb0295
     wherein R1k is H or C1-25 alkyl and R2k is OH or -OC1-12 alkyl.
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-9):
    Figure imgb0296
    • wherein R1m is H, OH, -CONH2, -COOH, -NHC(O)-C1-6 alkyl,-NHC(O)O-C1-6 alkyl,-NHS(O)2-C1-6alkyl, -C1-6 alkyl, -C1-6 alkoxyl, or -NHC(O)NH-C1-6alkyl;
    • R2m is H, CN, or CONH2; and
    • R3m is an optionally substituted C6-10 aryl.
  • In certain embodiments, the protein binding moiety is a residue of a compound having the structure of Formula (C-10):
    Figure imgb0297
    • wherein R1n is an optionally substituted C6-10 aryl or optionally substituted 5- to 10-membered heteroaryl, and
    • each R2n and R3n are independently H, -C1-4 alkyl-C6-10 aryl, -C1-4alkyl-5-to 10-membered heteroaryl, C6-10 aryl, or -5-to 10-membered heteroaryl, or
    • R2n and R3n together with N form an optionally substituted 4-10 membered heterocyclic or heteroaryl group.
  • In certain embodiments, the regulatory molecule is not a bromodomain-containing protein chosen from BRD2, BRD3, BRD4, and BRDT.
  • In certain embodiments, the regulatory molecule is BRD4. In certain embodiments, the recruiting moiety is a BRD4 activator. In certain embodiments, the BRD4 activator is chosen from JQ-1, OTX015, RVX208 acid, and RVX208 hydroxyl.
    Figure imgb0298
  • In certain embodiments, the regulatory molecule is BPTF. In certain embodiments, the recruiting moiety is a BPTF activator. In certain embodiments, the BPTF activator is AU1.
    Figure imgb0299
  • In certain embodiments, the regulatory molecule is histone acetyltransferase ("HAT"). In certain embodiments, the recruiting moiety is a HAT activator. In certain embodiments, the HAT activator is a oxopiperazine helix mimetic OHM. In certain embodiments, the HAT activator is selected from OHM1, OHM2, OHM3, and OHM4 (BB Lao et al., PNAS USA 2014, 111(21), 7531-7536). In certain embodiments, the HAT activator is OHM4.
    Figure imgb0300
  • In certain embodiments, the regulatory molecule is histone deacetylase ("HDAC"). In certain embodiments, the recruiting moiety is an HDAC activator. In certain embodiments, the HDAC activator is chosen from SAHA and 109 (Soragni E Front. Neurol. 2015, 6, 44, and references therein).
    Figure imgb0301
  • In certain embodiments, the regulatory molecule is histone deacetylase ("HDAC"). In certain embodiments, the recruiting moiety is an HDAC inhibitor. In certain embodiments, the HDAC inhibitor is an inositol phosphate.
  • In certain embodiments, the regulatory molecules is O-linked β-N-acetylglucosamine transferase ("OGT"). In certain embodiments, the recruiting moiety is an OGT activator. In certain embodiments, the OGT activator is chosen from ST045849, ST078925, and ST060266 (Itkonen HM, "Inhibition of O-GlcNAc transferase activity reprograms prostate cancer cell metabolism", Oncotarget 2016, 7(11), 12464-12476).
    Figure imgb0302
  • In certain embodiments, the regulatory molecule is chosen from host cell factor 1 ("HCF1") and octamer binding transcription factor ("OCT1"). In certain embodiments, the recruiting moiety is chosen from an HCF1 activator and an OCT1 activator. In certain embodiments, the recruiting moiety is chosen from VP16 and VP64.
  • In certain embodiments, the regulatory molecule is chosen from CBP and P300. In certain embodiments, the recruiting moiety is chosen from a CBP activator and a P300 activator. In certain embodiments, the recruiting moiety is CTPB.
    Figure imgb0303
  • In certain embodiments, the regulatory molecule is P300/CBP-associated factor ("PCAF"). In certain embodiments, the recruiting moiety is a PCAF activator. In certain embodiments, the PCAF activator is embelin.
    Figure imgb0304
  • In certain embodiments, the regulatory molecule modulates the rearrangement of histones.
  • In certain embodiments, the regulatory molecule modulates the glycosylation, phosphorylation, alkylation, or acylation of histones.
  • In certain embodiments, the regulatory molecule is a transcription factor.
  • In certain embodiments, the regulatory molecule is an RNA polymerase.
  • In certain embodiments, the regulatory molecule is a moiety that regulates the activity of RNA polymerase.
  • In certain embodiments, the regulatory molecule interacts with TATA binding protein.
  • In certain embodiments, the regulatory molecule interacts with transcription factor II D.
  • In certain embodiments, the regulatory molecule comprises a CDK9 subunit.
  • In certain embodiments, the regulatory molecule is P-TEFb.
  • In certain embodiments, X binds to the regulatory molecule but does not inhibit the activity of the regulatory molecule. In certain embodiments, X binds to the regulatory molecule and inhibits the activity of the regulatory molecule. In certain embodiments, X binds to the regulatory molecule and increases the activity of the regulatory molecule.
  • In certain embodiments, X binds to the active site of the regulatory molecule. In certain embodiments, X binds to a regulatory site of the regulatory molecule.
  • In certain embodiments, the recruiting moiety is chosen from a CDK-9 inhibitor, a cyclin T1 inhibitor, and a PRC2 inhibitor.
  • In certain embodiments, the recruiting moiety is a CDK-9 inhibitor. In certain embodiments, the CDK-9 inhibitor is chosen from flavopiridol, CR8, indirubin-3'-monoxime, a 5-fluoro-N2,N4-diphenylpyrimidine-2,4-diamine, a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine, TG02, CDKI-73, a 2,4,5-trisubstited pyrimidine derivatives, LCD000067, Wogonin, BAY-1000394 (Roniciclib), AZD5438, and DRB (F Morales et al. "Overview of CDK9 as a target in cancer research", Cell Cycle 2016, 15(4), 519-527, and references therein).
    Figure imgb0305
    Figure imgb0306
    Figure imgb0307
    Figure imgb0308
  • In certain embodiments, the regulatory molecule is a histone demethylase. In certain embodiments, the histone demethylase is a lysine demethylase. In certain embodiments, the lysine demethylase is KDM5B. In certain embodiments, the recruiting moiety is a KDM5B inhibitor. In certain embodiments, the KDM5B inhibitor is AS-8351 (N. Cao, Y. Huang, J. Zheng,et al., "Conversion of human fibroblasts into functional cardiomyocytes by small molecules", Science 2016, 352(6290),1216-1220, and references therein.)
    Figure imgb0309
  • In certain embodiments, the regulatory molecule is the complex between the histone lysine methyltransferases ("HKMT") GLP and G9A ("GLP/G9A"). In certain embodiments, the recruiting moiety is a GLP/G9A inhibitor. In certain embodiments, the GLP/G9A inhibitor is BIX-01294 (Chang Y, "Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294", Nature Struct. Mol. Biol. 2009, 16, 312-317, and references therein).
    Figure imgb0310
  • In certain embodiments, the regulatory molecule is a DNA methyltransferase ("DNMT"). In certain embodiments, the regulatory moiety is DNMT1. In certain embodiments, the recruiting moiety is a DNMT1 inhibitor. In certain embodiments, the DNMT1 inhibitor is chosen from RG108 and the RG108 analogues 1149, T1, and G6. (B Zhu et al. BioorgMed Chem 2015, 23(12), 2917-2927 and references therein).
    Figure imgb0311
    Figure imgb0312
  • In certain embodiments, the recruiting moiety is a PRC1 inhibitor. In certain embodiments, the PRC1 inhibitor is chosen from UNC4991, UNC3866, and UNC3567 (JI Stuckey et al. Nature Chem Biol 2016, 12(3), 180-187 and references therein; KD Bamash et al. ACS Chem. Biol. 2016, 11(9), 2475-2483, and references therein).
    Figure imgb0313
    Figure imgb0314
    Figure imgb0315
  • In certain embodiments, the recruiting moiety is a PRC2 inhibitor. In certain embodiments, the PRC2 inhibitor is chosen from A-395, MS37452, MAK683, DZNep, EPZ005687, EI1, GSK126, and UNC1999 (Konze KD ACS Chem Biol 2013, 8(6), 1324-1334, and references therein).
    Figure imgb0316
    Figure imgb0317
    Figure imgb0318
    Figure imgb0319
  • In certain embodiments, the recruiting moiety is rohitukine or a derivative of rohitukine.
  • In certain embodiments, the recruiting moiety is DB08045 or a derivative of DB08045.
    Figure imgb0320
  • In certain embodiments, the recruiting moiety is A-395 or a derivative of A-395.
  • In certain embodiments, the regulatory molecule is chosen from a bromodomain-containing protein, a nucleosome remodeling factor (NURF), a bromodomain PHD finger transcription factor (BPTF), a ten-eleven translocation enzyme (TET), methylcytosine dioxygenase (TET1), a DNA demethylase, a helicase, an acetyltransferase, and a histone deacetylase ("HDAC").
  • In certain embodiments, the regulatory molecule is a bromodomain-containing protein chosen from BRD2, BRD3, BRD4, and BRDT.
  • In certain embodiments, the regulatory molecule is BRD4. In certain embodiments, the recruiting moiety is a BRD4 activator. In certain embodiments, the BRD4 activator is chosen from JQ-1, OTX015, RVX208 acid, and RVX208 hydroxyl.
    Figure imgb0321
  • In certain embodiments, the regulatory molecule is BPTF. In certain embodiments, the recruiting moiety is a BPTF activator. In certain embodiments, the BPTF activator is AU1.
    Figure imgb0322
  • In certain embodiments, the regulatory molecule is histone acetyltransferase ("HAT"). In certain embodiments, the recruiting moiety is a HAT activator. In certain embodiments, the HAT activator is a oxopiperazine helix mimetic OHM. In certain embodiments, the HAT activator is selected from OHM1, OHM2, OHM3, and OHM4 (BB Lao et al., PNAS USA 2014, 111(21), 7531-7536). In certain embodiments, the HAT activator is OHM4.
    Figure imgb0323
  • In certain embodiments, the regulatory molecule is histone deacetylase ("HDAC"). In certain embodiments, the recruiting moiety is an HDAC activator. In certain embodiments, the HDAC activator is chosen from SAHA and 109 (Soragni E Front. Neurol. 2015, 6, 44, and references therein).
    Figure imgb0324
  • In certain embodiments, the regulatory molecule is histone deacetylase ("HDAC"). In certain embodiments, the recruiting moiety is an HDAC inhibitor. In certain embodiments, the HDAC inhibitor is an inositol phosphate.
  • In certain embodiments, the regulatory molecules is O-linked β-N-acetylglucosamine transferase ("OGT"). In certain embodiments, the recruiting moiety is an OGT activator. In certain embodiments, the OGT activator is chosen from ST045849, ST078925, and ST060266 (Itkonen HM, "Inhibition of O-GlcNAc transferase activity reprograms prostate cancer cell metabolism", Oncotarget 2016, 7(11), 12464-12476).
    Figure imgb0325
  • In certain embodiments, the regulatory molecule is chosen from host cell factor 1 ("HCF1") and octamer binding transcription factor ("OCT1"). In certain embodiments, the recruiting moiety is chosen from an HCF1 activator and an OCT1 activator. In certain embodiments, the recruiting moiety is chosen from VP16 and VP64.
  • In certain embodiments, the regulatory molecule is chosen from CBP and P300. In certain embodiments, the recruiting moiety is chosen from a CBP activator and a P300 activator. In certain embodiments, the recruiting moiety is CTPB.
    Figure imgb0326
  • In certain embodiments, the regulatory molecule is P300/CBP-associated factor ("PCAF"). In certain embodiments, the recruiting moiety is a PCAF activator. In certain embodiments, the PCAF activator is embelin.
    Figure imgb0327
  • In certain embodiments, the regulatory molecule modulates the rearrangement of histones.
  • In certain embodiments, the regulatory molecule modulates the glycosylation, phosphorylation, alkylation, or acylation of histones.
  • In certain embodiments, the regulatory molecule is a transcription factor.
  • In certain embodiments, the regulatory molecule is an RNA polymerase.
  • In certain embodiments, the regulatory molecule is a moiety that regulates the activity of RNA polymerase.
  • In certain embodiments, the regulatory molecule interacts with TATA binding protein.
  • In certain embodiments, the regulatory molecule interacts with transcription factor II D.
  • In certain embodiments, the regulatory molecule comprises a CDK9 subunit.
  • In certain embodiments, the regulatory molecule is P-TEFb.
  • In certain embodiments, the recruiting moiety binds to the regulatory molecule but does not inhibit the activity of the regulatory molecule. In certain embodiments, the recruiting moiety binds to the regulatory molecule and inhibits the activity of the regulatory molecule. In certain embodiments, the recruiting moiety binds to the regulatory molecule and increases the activity of the regulatory molecule.
  • In certain embodiments, the recruiting moiety binds to the active site of the regulatory molecule. In certain embodiments, the recruiting moiety binds to a regulatory site of the regulatory molecule.
  • In certain embodiments, the recruiting moiety is chosen from a CDK-9 inhibitor, a cyclin T1 inhibitor, and a PRC2 inhibitor.
  • In certain embodiments, the recruiting moiety is a CDK-9 inhibitor. In certain embodiments, the CDK-9 inhibitor is chosen from flavopiridol, CR8, indirubin-3'-monoxime, a 5-fluoro-N2,N4-diphenylpyrimidine-2,4-diamine, a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine, TG02, CDKI-73, a 2,4,5-trisubstited pyrimidine derivatives, LCD000067, Wogonin, BAY-1000394 (Roniciclib), AZD5438, and DRB (F Morales et al. "Overview of CDK9 as a target in cancer research", Cell Cycle 2016, 15(4), 519-527, and references therein).
    Figure imgb0328
    Figure imgb0329
    Figure imgb0330
    Figure imgb0331
  • In certain embodiments, the regulatory molecule is a histone demethylase. In certain embodiments, the histone demethylase is a lysine demethylase. In certain embodiments, the lysine demethylase is KDM5B. In certain embodiments, the recruiting moiety is a KDM5B inhibitor. In certain embodiments, the KDM5B inhibitor is AS-8351 (N. Cao, Y. Huang, J. Zheng,et al., "Conversion of human fibroblasts into functional cardiomyocytes by small molecules", Science 2016, 352(6290),1216-1220, and references therein.)
    Figure imgb0332
  • In certain embodiments, the regulatory molecule is the complex between the histone lysine methyltransferases ("HKMT") GLP and G9A ("GLP/G9A"). In certain embodiments, the recruiting moiety is a GLP/G9A inhibitor. In certain embodiments, the GLP/G9A inhibitor is BIX-01294 (Chang Y, "Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294", Nature Struct. Mol. Biol. 2009, 16, 312-317, and references therein).
    Figure imgb0333
  • In certain embodiments, the regulatory molecule is a DNA methyltransferase ("DNMT"). In certain embodiments, the regulatory moiety is DNMT1. In certain embodiments, the recruiting moiety is a DNMT1 inhibitor. In certain embodiments, the DNMT1 inhibitor is chosen from RG108 and the RG108 analogues 1149, T1, and G6. (B Zhu et al. BioorgMed Chem 2015, 23(12), 2917-2927 and references therein).
    Figure imgb0334
    Figure imgb0335
  • In certain embodiments, the recruiting moiety is a PRC1 inhibitor. In certain embodiments, the PRC1 inhibitor is chosen from UNC4991, UNC3866, and UNC3567 (JI Stuckey et al. Nature Chem Biol 2016, 12(3), 180-187 and references therein; KD Barnash et al. ACS Chem. Biol. 2016, 11(9), 2475-2483, and references therein).
    Figure imgb0336
    Figure imgb0337
    Figure imgb0338
  • In certain embodiments, the recruiting moiety is a PRC2 inhibitor. In certain embodiments, the PRC2 inhibitor is chosen from A-395, MS37452, MAK683, DZNep, EPZ005687, EI1, GSK126, and UNC1999 (Konze KD ACS Chem Biol 2013, 8(6), 1324-1334, and references therein).
    Figure imgb0339
    Figure imgb0340
    Figure imgb0341
    Figure imgb0342
  • In certain embodiments, the recruiting moiety is rohitukine or a derivative of rohitukine.
  • In certain embodiments, the recruiting moiety is DB08045 or a derivative of DB08045.
    Figure imgb0343
  • In certain embodiments, the recruiting moiety is A-395 or a derivative of A-395.
    • Oligomeric Backbone and Linker
  • The Oligomeric backbone contains a linker that connects the first terminus and the second terminus and brings the regulatory molecule in proximity to the target gene to modulate gene expression.
  • The length of the linker depends on the type of regulatory protein and also the target gene. In some embodiments, the linker has a length of less than about 50 Angstroms. In some embodiments, the linker has a length of about 20 to 30 Angstroms.
  • In some embodiments, the linker comprises between 5 and 50 chain atoms.
  • In some embodiments, the linker comprises a multimer having 2 to 50 spacing moieties, wherein the spacing moiety is independently selected from the group consisting of -((CR3aR3b)x-O)y-, - ((CR3aR3b)x-NR4a)y-, -((CR3aR3b)x-CH=CH-(CR3aR3b)x-O)y-, optionally substituted -C1-12 alkyl, optionally substituted C2-10 alkenyl, optionally substituted C2-10 alkynyl, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, optionally substituted 4- to 10-membered heterocycloalkylene, amino acid residue, -O-, -C(O)NR4a-, - NR4aC(O)-, -C(O)-, -NR4a-,-C(O)O-,-O-, -S-, -S(O)-, -SO2-, -SO2NR4-, - NR4aSO2-, and -P(O)OH-, and any combinations thereof, wherein
    • each x is independently 2-4;
    • each y is independently 1-10;
    • each R3a and R3b are independently selected from hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, optionally substituted alkylamide, sulfonyl, optionally substituted thioalkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl, and optionally substituted heterocyclyl; and
    • each R4a is independently a hydrogen or an optionally substituted C1-6 alkyl.
  • In some embodiments, the oligomeric backbone comprises -(T1-V1)a-(T2-V2)b-(T3-V3)c-(T4-V4)d-(T5-V5)e-,
    • wherein a, b, c, d and e are each independently 0 or 1, and where the sum of a, b, c, d and e is 1 to 5;
    • T1, T2, T3, T4 and T5 are each independently selected from an optionally substituted (C1-C12)alkylene, optionally substituted alkenylene, optionally substituted alkynylene, (EA)w, (EDA)m, (PEG)n, (modified PEG)n, (AA)p, -(CR2aOH)h-,optionally substituted (C6-C10) arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10 membered heteroarylene, optionally substituted 4- to 10-membered heterocycloalkylene, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, and an ester,
      1. (a) w is an integer from 1 to 20;
      2. (b) m is an integer from 1 to 20;
      3. (c) n is an integer from 1 to 30;
      4. (d) p is an integer from 1 to 20;
      5. (e) h is an integer from 1 to 12;
      6. (f) EA has the following structure
        Figure imgb0344
      7. (g) EDA has the following structure:
        Figure imgb0345
         wherein each q is independently an integer from 1 to 6, each x is independently an integer from 1 to 4, and each r is independently 0 or 1;
      8. (h) (PEG)n has the structure of -(CR2aR2b-CR2aR2b-O)n-CR2aR2b-;-
      9. (i) (modified PEG)n has the structure of replacing at least one -(CR2aR2b-CR2aR2b-O)- in (PEG)n with -(CH2-CR2a=CR2a-CH2-O)- or -(CR2aR2b-CR2aR2b-S)-;
      10. (j) AA is an amino acid residue;
      11. (k) V1, V2, V3, V4 and V3 are each independently selected from the group consisting of a bond, CO-, -NR1a-,-CONR1a-, -NR1aCO-, -CONR1aC1-4 alkyl-, -NR1aCO-C1-4 alkyl-, -C(O)O-, -OC(O)-, -O-, -S-, - S(O)-, -SO2-, -SO2NR1a-, -NR1aSO2- and -P(O)OH-;
      12. (l) each R1a is independently hydrogen or and optionally substituted C1-6 alkyl; and
      13. (m) each R2a and R2b are independently selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, halogen, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl.
  • In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 1. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 2. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 3. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 4. In some embodiments, the a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 5.
  • In some embodiments, n is 3-9. In some embodiments, n is 4-8. In some embodiments, n is 5 or 6.
  • In some embodiments, T1, T2, T3, and T4, and T5 are each independently selected from (C1-C12)alkyl, substituted (C1-C12)alkyl, (EA)w, (EDA)m, (PEG)n, (modified PEG)n, (AA)p, -(CR2aOH)h-, phenyl, substituted phenyl, piperidin-4-amino (P4A), para-amino-benzyloxycarbonyl (PABC), meta-amino-benzyloxycarbonyl (MABC), para-amino-benzyloxy (PABO), meta-amino-benzyloxy (MABO), paraaminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA)p-MABC-(AA)p, (AA)p-MABO-(AA)p, (AA)p-PABO-(AA)p and (AA)p-PABC-(AA)p, In some embodiments, piperidin-4-amino (P4A) is
    Figure imgb0346
     wherein R1a is H or C1-6 alkyl.
  • In some embodiments, T1, T2, T3, T4 and T5 are each independently selected from (C1-C12)alkyl, substituted (C1-C12)alkyl, (EA)w, (EDA)m, (PEG)n, (modified PEG)n, (AA)p,-(CR2aOH)h-, optionally substituted (C6-C10) arylene, 4-10 membered heterocycloalkene, optionally substituted 5-10 membered heteroarylene. In some embodiments, EA has the following structure:
    Figure imgb0347
     and EDA has the following structure:
    Figure imgb0348
  • In some embodiments, x is 2-3 and q is 1-3 for EA and EDA. In some embodiments, R1a is H or C1-6 alkyl.
  • In some embodiments, T4 or T5 is an optionally substituted (C6-C10) arylene.
  • In some embodiments, T4 or T5 is phenylene or substituted phenylene. In some embodiments, T4 or T5 is phenylene or phenylene substituted with 1-3 substituents selected from -C1-6 alkyl, halogen, OH or amine. In some embodiments, T4 or T5 is 5-10 membered heteroarylene or substituted heteroarylene. In some embodiments, T4 or T5 is 4-10 membered heterocylcylene or substituted heterocylcylene. In some embodiments, T4 or T5 is heteroarylene or heterocylcylene optionally substituted with 1-3 substituents selected from -C1-6 alkyl, halogen, OH or amine.
  • In some embodiments, T1, T2, T3, T4 and T5 and V1, V2, V3, V4 and V5 are selected from the following Table 6:
    T1 V1 T2 V2 T3 V3 T4 V4 T5 V5
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n NR11CO ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG). O arylene NR11CO ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG). O Subst. arylene NR11CO ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O NR11C O (C1-C12) alkyl Subst. arvlene NR11CO
    (C1-C12) alkylene CONR1a (EA)w CO (C1-C12) alkyl NR11CO-C1-4 alkyl Subst. arylene NR11 ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O Subst. arylene ---- ---- ----
    (PEG)n CONR1a- C1-4 alkyl ---- ---- ---- ---- ---- ---- ---- ----
    (EA)w CO (C1-C12) alkyl CONR11- C1-4 alkvl ---- ---- ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG). NR11CO-C1-4 alkyl ---- ---- ---- ----
    (EA)w CO (PEG)n O phenyl NR11CO-C1-4 alkyl ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (PEG)n CO ---- ---- ---- ---- ---- ----
    (C1-C12) alkvlene CONR1a (EA)w CO modifd. (PEG)n O arylene NR11CO ---- ----
  • In some embodiments, the linker comprises
    Figure imgb0349
     or any combinations thereof, wherein r is an integer between 1 and 10, preferably between 3 and 7; and X is O, S, or NR1a. In some embodiments, X is O or NR1a. In some embodiments, X is O.
  • In some embodiments, the linker comprise a
    Figure imgb0350
     or any combinations thereof; wherein at least one -(CH2-CH2-O)- is replaced with -(CR1aR1b)x-CH=CH-(CR1aR1b)x -O)-, or any combinations thereof; W' is absent, (CH2)1-5, -(CH2)1-5O, (CH2)1-5-C(O)NH-(CH2)1-5-O, (CH2)1-5-C(O)NH-(CH2)1-5, -(CH2)1-5NHC(O)-(CH2)1-5-O, or -(CH2)1-5-NHC(O)-(CH2)1-5-; E3 is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocycloalkylene, or optionally substituted 5-10 membered heteroarylene; X is O, S, or NH; each R1a and R1b are independently H or C1-6 alkyl; r is an integer between 1 and 10; and x is an integer between 1 and 15. In some embodiments, X is O. In some embodiments, X is NH. In some embodiments, E3 is a C6-10 arylene group optionally substituted with 1-3 substituents selected from -C1-6 alkyl, halogen, OH or amine.
  • In some embodiments, E3 is a phenylene or substituted phenylene.
  • In some embodiments, the linker comprise a
    Figure imgb0351
    Figure imgb0352
  • In some embodiments, the linker comprises -X(CH2)m(CH2CH2O)n-, wherein X is -O-, NH-, or - S-, wherein m is 0 or greater and n is at least 1.
  • In some embodiments, the linker comprises
    Figure imgb0353
     following the second terminus, wherein Rc is selected from a bond, -N(R1a)-, -O-, and -S-; Rd is selected from -N(R1a)-, -O-, and -S-; and Rc is independently selected from hydrogen and optionally substituted C1-6 alkyl
  • In some embodiments, the linker comprises one or more structures selected from
    Figure imgb0354
     ,
    Figure imgb0355
     -C1-12 alkyl, arylene, cycloalkylene, heteroarylene, heterocycloalkylene, -O-, -C(O)NR1a-,-C(O)-, -NR1a-, -(CH2CH2CH2O)y-, and -(CH2CH2CH2NR1a)y- wherein each d and y are independently 1-10, andeach R1a is independently hydrogen or C1-6 alkyl. In some embodiments, d is 4-8.
  • In some embodiments, the linker comprises
    Figure imgb0356
     and each d is independently 3-7. In some embodiments, d is 4-6.
  • In some embodiments, the linker comprises N(R1a)(CH2)xN(R1b)(CH2)xN-, wherein R1a andR1b are each independently selected from hydrogen or optionally substituted C1-C6 alkyl; and each x is independently an integer in the range of 1-6..
  • In some embodiments, the linker comprises the linker comprises -(CH2 -C(O)N(R")-(CH2)q-N(R')-(CH2)q-N(R")C(O)-(CH2)x-C(O)N(R")-A-, -(CH2)x-C(O)N(R")-(CH2 CH2O)y(CH2)x-C(O)N(R")-A-, - C(O)N(R")-(CH2)q-N(R')-(CH2)q-N(R")C(O)-(CH2)x-A-, -(CH2)x-O-(CH2 CH2O)y-(CH2)x-N(R")C(O)-(CH2)x-A-, or -N(R")C(O)-(CH2)-C(O)N(R")-(CH2)x-O(CH2CH2O)y(CH2)x-A-; wherein R' is methyl; R" is hydrogen; each x and y are independently an integer from 1 to 10; each q is independently an integer from 2 to 10; and each A is independently selected from a bond, an optionally substituted C1-12 alkyl, an optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene.
  • In some embodiments, the linker is joined with the first terminus with a group selected from - CO-, -NR1a-,-CONR1a-, -NR1aCO-, -CONR1aC1-4alkyl-, -NR1aCO-C1-4alkyl -, -C(O)O-, -OC(O)-, -O-, -S-, -S(O)-, -SO2-, -SO2NR1a-, -NR1SO2-, -P(O)OH-,-((CH2)x-O)-, -((CH2)y-NR1a-, optionally substituted -C1-12 alkylene, optionally substituted C2-10 alkenylene, optionally substituted C2-10 alkynylene, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene, wherein each x is independently 1-4, each y is independently 1-4, and each R1a is independently a hydrogen or optionally substituted C1-6 alkyl.
  • ln some embodiments, the linker is joined with the first terminus with a group selected from - CO-, -NR1a-,C1-12alkyl, -CONR1a-, and -NR1aCO-.
  • In some embodiments, the linker is joined with second terminus with a group selected from —CO—, -NR1a-,-CONR1a-, -NR1aCO-, -CONR1aC1-4alkyl-, -NR1aCO-C1-4alkyl -, -C(O)O-, - OC(O)-, -O-, -S-, -S(O)-, -SO2-, -SO2NR1a-, -NR1SO2-, -P(O)OH-,-((CH2)x-O)-, -((CH2)y-NR1a)-, optionally substituted -C1-12 alkylene, optionally substituted C2-10 alkenylene, optionally substituted C2-10 alkynylene, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene, wherein each x is independently 1-4, each y is independently 1-4, and each R1a is independently a hydrogen or optionally substituted C1-6 alkyl.
  • ln some embodiments, the linker is joined with second terminus with a group selected from —CO—, -NR1a-, -CONR1a-, -NR1aCO-,-((CH2)x-O)-, -((CH2)y-NR1a)-, -O-, optionally substituted -C1-12 alkyl, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene, wherein each x is independently 1-4, each y is independently 1-4, and each R' is independently a hydrogen or optionally substituted C1-6 alkyl.
    • Cell-penetrating ligand
  • In certain embodiments, the compounds comprise a cell-penetrating ligand moiety.
  • In certain embodiments, the cell-penetrating ligand moiety is a polypeptide.
  • In certain embodiments, the cell-penetrating ligand moiety is a polypeptide containing fewer than 30 amino acid residues.
  • In certain embodiments, the polypeptide is chosen from any one of SEQ ID NO. 1 to SEQ ID NO. 37, inclusive.
  • In some embodiments, the second terminus does not comprise a structure of Formula (C-11):
    Figure imgb0357
     wherein:
    • each of A1p and B1p is independently an optionally substituted aryl or heteroaryl ring;
    • X1p is CH or N;
    • R1p is hydrogen, halogen, or an optionally substituted C1-6 alkyl group; and
    • R2p is an optionally substituted C1-6 alkyl, cycloalkyl, C6-10 aryl, or heteroaryl.
  • In some ebmbodiments, the protein binding moiety does not have the structure of Formula (C-12):
    Figure imgb0358
     wherein:
    • R1q is a hydrogen or an optionally substituted alkyl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, halogenated alkyl, hydroxyl, alkoxy, or -COOR4q;
    • R4q is hydrogen, or an optionally substituted aryl, aralkyl, cycloalkyl, heteroaryl, heteroaralkyl, heterocycloalkyl, alkyl, alkenyl, alkynyl, or cycloalkylalkyl group, optionally containing one or more heteroatoms;
    • R2q is an optionally substituted aryl, alkyl, cycloalkyl, or aralkyl group;
    • R3q is hydrogen, halogen, or an optionally substituted alkyl group, preferably (CH2)x - C(O)N(R20)(R21), or (CH2)x-N(R20)-C(O)R21; or halogenated alkyl group;
    • wherein x is an integer from 1 to 10; and R20 and R21 are each independently hydrogen or C1-C6 alkyl group, preferably R20 is hydrogen and R21 ismethyl; and
    • Ring E is an optionally substituted aryl or heteroaryl group.
  • Also provided are embodiments wherein any compound disclosed above, including compounds of Formulas A1-A10, C1-C11, and I - VII, are singly, partially, or fully deuterated. Methods for accomplishing deuterium exchange for hydrogen are known in the art
  • Also provided are embodiments wherein any embodiment above may be combined with any one or more of these embodiments, provided the combination is not mutually exclusive.
  • As used herein, two embodiments are "mutually exclusive" when one is defined to be something which is different than the other. For example, an embodiment wherein two groups combine to form a cycloalkyl is mutually exclusive with an embodiment in which one group is ethyl the other group is hydrogen. Similarly, an embodiment wherein one group is CH2 is mutually exclusive with an embodiment wherein the same group is NH.
    • Method of Treatment
  • The present disclosure also relates to a method of modulating the transcription of fxncomprising the step of contacting fxnwith a compound as described herein. The cell phenotype, cell proliferation, transcription of fxn, production of mRNA from transcription of fxn, translation of fxn, change in biochemical output produced by the protein coded by fxn, or noncovalent binding of the protein coded by fxn with a natural binding partner may be monitored. Such methods may be modes of treatment of disease, biological assays, cellular assays, biochemical assays, or the like.
  • Also provided herein is a method of treatment of a disease mediated by transcription of fxn comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt thereof, to a patient in need thereof.
  • In certain embodiments, the disease is Friedreich's ataxia..
  • Also provided herein is a compound as disclosed herein for use as a medicament.
  • Also provided herein is a compound as disclosed herein for use as a medicament for the treatment of a disease mediated by transcription of fxn.
  • Also provided is the use of a compound as disclosed herein as a medicament.
  • Also provided is the use of a compound as disclosed herein as a medicament for the treatment of a disease mediated by transcription of fxn.
  • Also provided is a compound as disclosed herein for use in the manufacture of a medicament for the treatment of a disease mediated by transcription of fxn.
  • Also provided is the use of a compound as disclosed herein for the treatment of a disease mediated by transcription of fxn.
  • Also provided herein is a method of modulation of transcription of fxn comprising contacting fxn with a compound as disclosed herein, or a salt thereof.
  • Also provided herein is a method for achieving an effect in a patient comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt thereof, to a patient, wherein the effect is chosen from improved neural sensation, improved vision, improved balance, improved gait, reduced sensitivity to glucose, and reduced sensitivity to carbohydrates.
  • Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 5 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 10 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 20 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 50 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 100 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 200 or more repeats of GAA. Certain compounds of the present disclosure may be effective for treatment of subjects whose genotype has 500 or more repeats of GAA.
  • Also provided is a method of modulation of a fxn-mediated function in a subject comprising the administration of a therapeutically effective amount of a compound as disclosed herein.
  • Also provided is a pharmaceutical composition comprising a compound as disclosed herein, together with a pharmaceutically acceptable carrier.
  • In certain embodiments, the pharmaceutical composition is formulated for oral administration.
  • In certain embodiments, the pharmaceutical composition is formulated for intravenous injection and/or infusion.
  • In certain embodiments, the oral pharmaceutical composition is chosen from a tablet and a capsule.
  • In certain embodiments, ex vivo methods of treatment are provided. Ex vivo methods typically include cells, organs, and/or tissues removed from the subject. The cells, organs and/or tissues can, for example, be incubated with the agent under appropriate conditions. The contacted cells, organs, and/or tissues are typically returned to the donor, placed in a recipient, or stored for future use. Thus, the compound is generally in a pharmaceutically acceptable carrier.
  • In certain embodiments, administration of the pharmaceutical composition modulates expression of fxnwithin 6 hours of treatment. In certain embodiments, administration of the pharmaceutical composition modulates expression of fxnwithin 24 hours of treatment. In certain embodiments, administration of the pharmaceutical composition modulates expression of fxnwithin 72 hours of treatment.
  • In certain embodiments, administration of the pharmaceutical composition causes a 2-fold increase in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 5-fold increase in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 10-fold increase in expression of fxnc9orf72. In certain embodiments, administration of the pharmaceutical composition causes a 20-fold increase in expression of fxn.
  • In certain embodiments, administration of the pharmaceutical composition causes a 20 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 50 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 80 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 90 % decrease in expression of fxn. In certain embodiments, administration of the pharmaceutical composition causes a 95 % decrease in expression of fxn2. In certain embodiments, administration of the pharmaceutical composition causes a 99 % decrease in expression of fxn.
  • In certain embodiments, administration of the pharmaceutical composition causes expression of c9orf72 to fall within 25 % of the level of expression observed for healthy individuals. In certain embodiments, administration of the pharmaceutical composition causes expression of fanto fall within 50 % of the level of expression observed for healthy individuals. In certain embodiments, administration of the pharmaceutical composition causes expression of fxnto fall within 75 % of the level of expression observed for healthy individuals. In certain embodiments, administration of the pharmaceutical composition causes expression of fxnto fall within 90 % of the level of expression observed for healthy individuals.
    • Pharmaceutical Composition and Administration
  • Also provided is a method of modulation of a fxn-mediated function in a subject comprising the administration of a therapeutically effective amount of a compound as disclosed herein.
  • Also provided is a pharmaceutical composition comprising a compound as disclosed herein, together with a pharmaceutically acceptable carrier.
  • In certain embodiments, the pharmaceutical composition is formulated for oral administration.
  • In certain embodiments, the pharmaceutical composition is formulated for intravenous injection or infusion.
  • In certain embodiments, the oral pharmaceutical composition is chosen from a tablet and a capsule.
  • In certain embodiments, ex vivo methods of treatment are provided. Ex vivo methods typically include cells, organs, or tissues removed from the subject. The cells, organs or tissues can, for example, be incubated with the agent under appropriate conditions. The contacted cells, organs, or tissues are typically returned to the donor, placed in a recipient, or stored for future use. Thus, the compound is generally in a pharmaceutically acceptable carrier.
  • In certain embodiments, the compound is effective at a concentration less than about 5 µM. In certain embodiments, the compound is effective at a concentration less than about 1 µM. In certain embodiments, the compound is effective at a concentration less than about 400 nM. In certain embodiments, the compound is effective at a concentration less than about 200 nM. In certain embodiments, the compound is effective at a concentration less than about 100 nM. In certain embodiments, the compound is effective at a concentration less than about 50 nM. In certain embodiments, the compound is effective at a concentration less than about 20 nM. In certain embodiments, the compound is effective at a concentration less than about 10 nM.
    • Abbreviations and Definitions
  • As used herein, the terms below have the meanings indicated.
  • lt is to be understood that certain radical naming conventions can include either a mono-radical or a di-radical, depending on the context. For example, where a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical. For example, a substituent identified as alkyl that requires two points of attachment includes di-radicals such as -CH2-, -CH2CH2-, - CH2CH(CH3)CH2-, and the like. Other radical naming conventions clearly indicate that the radical is a di-radical such as "alkylene," "alkenylene," "arylene", "heteroarylene."
  • When two R groups are said to form a ring (e.g., a carbocyclyl, heterocyclyl, aryl, or heteroaryl ring) "together with the atom to which they are attached," it is meant that the collective unit of the atom and the two R groups are the recited ring. The ring is not otherwise limited by the definition of each R group when taken individually. For example, when the following substructure is present:
    Figure imgb0359
     and R1 and R2 are defined as selected from the group consisting of hydrogen and alkyl, or R1 and R2 together with the nitrogen to which they are attached form a heterocyclyl, it is meant that R1 and R2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure:
    Figure imgb0360
     where ring A is a heteroaryl ring containing the depicted nitrogen.
  • Similarly, when two "adjacent" R groups are said to form a ring "together with the atom to which they are attached," it is meant that the collective unit of the atoms, intervening bonds, and the two R groups are the recited ring. For example, when the following substructure is present:
    Figure imgb0361
     and R1 and R2 are defined as selected from the group consisting of hydrogen and alkyl, or R1 and R2 together with the atoms to which they are attached form an aryl or carbocylyl, it is meant that R1 and R2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure:
    Figure imgb0362
     where A is an aryl ring or a carbocylyl containing the depicted double bond.
  • Wherever a substituent is depicted as a di-radical (i.e., has two points of attachment to the rest of the molecule), it is to be understood that the substituent can be attached in any directional configuration unless otherwise indicated. Thus, for example, a substituent depicted as AE- or
    Figure imgb0363
     includes the substituent being oriented such that the A is attached at the leftmost attachment point of the molecule as well as the case in which A is attached at the rightmost attachment point of the molecule.
  • When ranges of values are disclosed, and the notation "from n1 ... to n2" or "between n1 ... and n2" is used, where n1 and n2 are the numbers, then unless otherwise specified, this notation is intended to include the numbers themselves and the range between them. This range may be integral or continuous between and including the end values. By way of example, the range "from 2 to 6 carbons" is intended to include two, three, four, five, and six carbons, since carbons come in integer units. Compare, by way of example, the range "from 1 to 3 µM (micromolar)," which is intended to include 1 µM, 3 µM, and everything in between to any number of significant figures (e.g., 1.255 µM, 2.1 µM, 2.9999 µM, etc.).
  • The term "about," as used herein, is intended to qualify the numerical values which it modifies, denoting such a value as variable within a margin of error. When no particular margin of error, such as a standard deviation to a mean value given in a chart or table of data, is recited, the term "about" should be understood to mean that range which would encompass the recited value and the range which would be included by rounding up or down to that figure as well, taking into account significant figures.
  • The term "polyamide" refers to polymers of linkable units chemically bound by amide (i.e., CONH) linkages; optionally, polyamides include chemical probes conjugated therewith. Polyamides may be synthesized by stepwise condensation of carboxylic acids (COOH) with amines (RR'NH) using methods known in the art. Alternatively, polyamides may be formed using enzymatic reactions in vitro, or by employing fermentation with microorganisms.
  • The term "linkable unit" refers to methylimidazoles, methylpyrroles, and straight and branched chain aliphatic functionalities (e.g., methylene, ethylene, propylene, butylene, and the like) which optionally contain nitrogen Substituents, and chemical derivatives thereof. The aliphatic functionalities of linkable units can be provided, for example, by condensation of B-alanine or dimethylaminopropylaamine during synthesis of the polyamide by methods well known in the art.
  • The term "linker" refers to a chain of at least 10 contiguous atoms. In certain embodiments, the linker contains no more than 20 non-hydrogen atoms. In certain embodiments, the linker contains no more than 40 non-hydrogen atoms. In certain embodiments, the linker contains no more than 60 non-hydrogen atoms. In certain embodiments, the linker contains atoms chosen from C, H, N, O, and S. In certain embodiments, every non-hydrogen atom is chemically bonded either to 2 neighboring atoms in the linker, or one neighboring atom in the linker and a terminus of the linker. In certain embodiments, the linker forms an amide bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms an ester or ether bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms a thiolester or thioether bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms a direct carbon-carbon bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker forms an amine or amide bond with at least one of the two other groups to which it is attached. In certain embodiments, the linker comprises -(CH2OCH2)- units. In certain embodiments, the linker comprises -(CH(CH3)OCH2)- units. In certain embodiments, the linker comprises -(CH2NRNCH2) units, for RN = C1-4alkyl. In certain embodiments, the linker comprises an arylene, cycloalkylene, or heterocycloalkylene moiety.
  • The term "spacer" refers to a chain of at least 5 contiguous atoms. In certain embodiments, the spacer contains no more than 10 non-hydrogen atoms. In certain embodiments, the spacer contains atoms chosen from C, H, N, O, and S. In certain embodiments, the spacer forms amide bonds with the two other groups to which it is attached. In certain embodiments, the spacer comprises -(CH2OCH2)- units. In certain embodiments, the spacer comprises -(CH2NRNCH2)- units, for RN = C1-4alkyl. In certain embodiments, the spacer contains at least one positive charge at physiological pH.
  • The term "turn component" refers to a chain of about 4 to 10 contiguous atoms. In certain embodiments, the turn component contains atoms chosen from C, H, N, O, and S. In certain embodiments, the turn component forms amide bonds with the two other groups to which it is attached. In certain embodiments, the turn component contains at least one positive charge at physiological pH.
  • The terms "nucleic acid and "nucleotide" refer to ribonucleotide and deoxyribonucleotide, and analogs thereof, well known in the art.
  • The term "oligonucleotide sequence" refers to a plurality of nucleic acids having a defined sequence and length (e.g., 2, 3, 4, 5, 6, or even more nucleotides). The term "oligonucleotide repeat sequence" refers to a contiguous expansion of oligonucleotide sequences.
  • The term "transcription," well known in the art, refers to the synthesis of RNA (i.e., ribonucleic acid) by DNA-directed RNA polymerase. The term "modulate transcription" refers to a change in transcriptional level which can be measured by methods well known in the art, for example, assay of mRNA, the product of transcription. In certain embodiments, modulation is an increase in transcription. In other embodiments, modulation is a decrease in transcription
  • The term "acyl," as used herein, alone or in combination, refers to a carbonyl attached to an alkenyl, alkyl, aryl, cycloalkyl, heteroaryl, heterocycle, or any other moiety were the atom attached to the carbonyl is carbon. An "acetyl" group refers to a -C(O)CH3 group. An "alkylcarbonyl" or "alkanoyl" group refers to an alkyl group attached to the parent molecular moiety through a carbonyl group. Examples of such groups include methylcarbonyl and ethylcarbonyl. Examples of acyl groups include formyl, alkanoyl and aroyl.
  • The term "alkenyl," as used herein, alone or in combination, refers to a straight-chain or branchedchain hydrocarbon radical having one or more double bonds and containing from 2 to 20 carbon atoms. In certain embodiments, said alkenyl will comprise from 2 to 6 carbon atoms. The term "alkenylene" refers to a carbon-carbon double bond system attached at two or more positions such as ethenylene [(-CH=CH-),(-C::C-)]. Examples of suitable alkenyl radicals include ethenyl, propenyl, 2-methylpropenyl, 1,4-butadienyl and the like. Unless otherwise specified, the term "alkenyl" may include "alkenylene" groups.
  • The term "alkoxy," as used herein, alone or in combination, refers to an alkyl ether radical, wherein the term alkyl is as defined below. Examples of suitable alkyl ether radicals include methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, and the like.
  • The term "alkyl," as used herein, alone or in combination, refers to a straight-chain or branchedchain alkyl radical containing from 1 to 20 carbon atoms. In certain embodiments, said alkyl will comprise from 1 to 10 carbon atoms. In further embodiments, said alkyl will comprise from 1 to 8 carbon atoms. Alkyl groups may be optionally substituted as defined herein. Examples of alkyl radicals include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, iso-amyl, hexyl, octyl, noyl and the like. The term "alkylene," as used herein, alone or in combination, refers to a saturated aliphatic group derived from a straight or branched chain saturated hydrocarbon attached at two or more positions, such as methylene
    (-CH2-). Unless otherwise specified, the term "alkyl" may include "alkylene" groups.
  • The term "alkylamino," as used herein, alone or in combination, refers to an alkyl group attached to the parent molecular moiety through an amino group. Suitable alkylamino groups may be mono- or dialkylated, forming groups such as, for example, N-methylamino, N-ethylamino, N,N-dimethylamino, N,N-ethylmethylamino and the like.
  • The term "alkylidene," as used herein, alone or in combination, refers to an alkenyl group in which one carbon atom of the carbon-carbon double bond belongs to the moiety to which the alkenyl group is attached.
  • The term "alkylthio," as used herein, alone or in combination, refers to an alkyl thioether (R-S-) radical wherein the term alkyl is as defined above and wherein the sulfur may be singly or doubly oxidized. Examples of suitable alkyl thioether radicals include methylthio, ethylthio, n-propylthio, isopropylthio, n-butylthio, iso-butylthio, sec-butylthio, tert-butylthio, methanesulfonyl, ethanesulfinyl, and the like.
  • The term "alkynyl," as used herein, alone or in combination, refers to a straight-chain or branched chain hydrocarbon radical having one or more triple bonds and containing from 2 to 20 carbon atoms. In certain embodiments, said alkynyl comprises from 2 to 6 carbon atoms. In further embodiments, said alkynyl comprises from 2 to 4 carbon atoms. The term "alkynylene" refers to a carbon-carbon triple bond attached at two positions such as ethynylene (-C:::C-, -C≡C-). Examples of alkynyl radicals include ethynyl, propynyl, hydroxypropynyl, butyn-1-yl, butyn-2-yl, pentyn-1-yl, 3-methylbutyn-1-yl, hexyn-2-yl, and the like. Unless otherwise specified, the term "alkynyl" may include "alkynylene" groups.
  • The terms "amido" and "carbamoyl,"as used herein, alone or in combination, refer to an amino group as described below attached to the parent molecular moiety through a carbonyl group, or vice versa. The term "C-amido" as used herein, alone or in combination, refers to a -C(O)N(RR') group with R and R' as defined herein or as defined by the specifically enumerated "R" groups designated. The term "N-amido" as used herein, alone or in combination, refers to a RC(O)N(R')- group, with R and R' as defined herein or as defined by the specifically enumerated "R" groups designated. The term "acylamino" as used herein, alone or in combination, embraces an acyl group attached to the parent moiety through an amino group. An example of an "acylamino" group is acetylamino (CH3C(O)NH-).
  • The term "amide," as used herein, alone in combination, refers to -C(O)NRR', wherein R and R' are independently chosen from hydrogen, alkyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R' may combine to form heterocycloalkyl, either of which may be optionally substituted. Amides may be formed by direct condensation of carboxylic acids with amines, or by using acid chlorides. In addition, coupling reagents are known in the art, including carbodiimide-based compounds such as DCC and EDCI.
  • The term "amino," as used herein, alone or in combination, refers to -NRR, wherein R and R are independently chosen from hydrogen, alkyl, acyl, heteroalkyl, aryl, cycloalkyl, heteroaryl, and heterocycloalkyl, any of which may themselves be optionally substituted. Additionally, R and R' may combine to form heterocycloalkyl, either of which may be optionally substituted.
  • The term "aryl," as used herein, alone or in combination, means a carbocyclic aromatic system containing one, two or three rings wherein such polycyclic ring systems are fused together. The term "aryl" embraces aromatic groups such as phenyl, naphthyl, anthracenyl, and phenanthryl. The term "arylene" embraces aromatic groups such as phenylene, naphthylene, anthracenylene, and phenanthrylene.
  • The term "arylalkenyl" or "aralkenyl," as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkenyl group.
  • The term "arylalkoxy" or "aralkoxy," as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkoxy group.
  • The term "arylalkyl" or "aralkyl," as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkyl group.
  • The term "arylalkynyl" or "aralkynyl," as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an alkynyl group.
  • The term "arylalkanoyl" or "aralkanoyl" or "aroyl,"as used herein, alone or in combination, refers to an acyl radical derived from an aryl-substituted alkanecarboxylic acid such as benzoyl, napthoyl, phenylacetyl, 3-phenylpropionyl (hydrocinnamoyl), 4-phenylbutyryl, (2-naphthyl)acetyl, 4-chlorohydrocinnamoyl, and the like.
  • The term aryloxy as used herein, alone or in combination, refers to an aryl group attached to the parent molecular moiety through an oxy.
  • The terms "benzo" and "benz," as used herein, alone or in combination, refer to the divalent radical C6H4= derived from benzene. Examples include benzothiophene and benzimidazole.
  • The term "carbamate," as used herein, alone or in combination, refers to an ester of carbamic acid (-NHCOO-) which may be attached to the parent molecular moiety from either the nitrogen or acid end, and which may be optionally substituted as defined herein.
  • The term "O-carbamyl" as used herein, alone or in combination, refers to a -OC(O)NRR', group-with R and R' as defined herein.
  • The term "N-carbamyl" as used herein, alone or in combination, refers to a ROC(O)NR'- group, with R and R' as defined herein.
  • The term "carbonyl," as used herein, when alone includes formyl [-C(O)H] and in combination is a - C(O)- group.
  • The term "carboxyl" or "carboxy," as used herein, refers to -C(O)OH or the corresponding "carboxylate" anion, such as is in a carboxylic acid salt. An "O-carboxy" group refers to a RC(O)O- group, where R is as defined herein. A "C-carboxy" group refers to a -C(O)OR groups where R is as defined herein.
  • The term "cyano," as used herein, alone or in combination, refers to -CN.
  • The term "cycloalkyl," or, alternatively, "carbocycle," as used herein, alone or in combination, refers to a saturated or partially saturated monocyclic, bicyclic or tricyclic alkyl group wherein each cyclic moiety contains from 3 to 12 carbon atom ring members and which may optionally be a benzo fused ring system which is optionally substituted as defined herein. In certain embodiments, said cycloalkyl will comprise from 5 to 7 carbon atoms. Examples of such cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, tetrahydronapthyl, indanyl, octahydronaphthyl, 2,3-dihydro-1H-indenyl, adamantyl and the like. "Bicyclic" and "tricyclic" as used herein are intended to include both fused ring systems, such as decahydronaphthalene, octahydronaphthalene as well as the multicyclic (multicentered) saturated or partially unsaturated type. The latter type of isomer is exemplified in general by, bicyclo[1,1,1]pentane, camphor, adamantane, and bicyclo[3,2,1]octane.
  • The term "ester," as used herein, alone or in combination, refers to a carboxy group bridging two moieties linked at carbon atoms.
  • The term "ether," as used herein, alone or in combination, refers to an oxy group bridging two moieties linked at carbon atoms.
  • The term "halo," or "halogen," as used herein, alone or in combination, refers to fluorine, chlorine, bromine, or iodine.
  • The term "haloalkoxy," as used herein, alone or in combination, refers to a haloalkyl group attached to the parent molecular moiety through an oxygen atom.
  • The term "haloalkyl," as used herein, alone or in combination, refers to an alkyl radical having the meaning as defined above wherein one or more hydrogens are replaced with a halogen. Specifically embraced are monohaloalkyl, dihaloalkyl and polyhaloalkyl radicals. A monohaloalkyl radical, for one example, may have an iodo, bromo, chloro or fluoro atom within the radical. Dihalo and polyhaloalkyl radicals may have two or more of the same halo atoms or a combination of different halo radicals. Examples of haloalkyl radicals include fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl. "Haloalkylene" refers to a haloalkyl group attached at two or more positions. Examples include fluoromethylene (-CFH-), difluoromethylene (-CF2 -), chloromethylene (-CHCl-) and the like.
  • The term "heteroalkyl," as used herein, alone or in combination, refers to a stable straight or branched chain, or combinations thereof, fully saturated or containing from 1 to 3 degrees of unsaturation, consisting of the stated number of carbon atoms and from one to three heteroatoms chosen from N, O, and S, and wherein the N and S atoms may optionally be oxidized and the N heteroatom may optionally be quatemized. The heteroatom(s) may be placed at any interior position of the heteroalkyl group. Up to two heteroatoms may be consecutive, such as, for example, -CH2-NH-OCH3.
  • The term "heteroaryl," as used herein, alone or in combination, refers to a 3 to 15 membered unsaturated heteromonocyclic ring, or a fused monocyclic, bicyclic, or tricyclic ring system in which at least one of the fused rings is aromatic, which contains at least one atom chosen from N, O, and S. In certain embodiments, said heteroaryl will comprise from 1 to 4 heteroatoms as ring members. In further embodiments, said heteroaryl will comprise from 1 to 2 heteroatoms as ring members. In certain embodiments, said heteroaryl will comprise from 5 to 7 atoms. The term also embraces fused polycyclic groups wherein heterocyclic rings are fused with aryl rings, wherein heteroaryl rings are fused with other heteroaryl rings, wherein heteroaryl rings are fused with heterocycloalkyl rings, or wherein heteroaryl rings are fused with cycloalkyl rings. Examples of heteroaryl groups include pyrrolyl, pyrrolinyl, imidazolyl, pyrazolyl, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazolyl, pyranyl, furyl, thienyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, thiadiazolyl, isothiazolyl, indolyl, isoindolyl, indolizinyl, benzimidazolyl, quinolyl, isoquinolyl, quinoxalinyl, quinazolinyl, indazolyl, benzotriazolyl, benzodioxolyl, benzopyranyl, benzoxazolyl, benzoxadiazolyl, benzothiazolyl, benzothiadiazolyl, benzofuryl, benzothienyl, chromonyl, coumarinyl, benzopyranyl, tetrahydroquinolinyl, tetrazolopyridazinyl, tetrahydroisoquinolinyl, thienopyridinyl, furopyridinyl, pyrrolopyridinyl and the like. Exemplary tricyclic heterocyclic groups include carbazolyl, benzidolyl, phenanthrolinyl, dibenzofuranyl, acridinyl, phenanthridinyl, xanthenyl and the like.
  • The terms "heterocycloalkyl" and, interchangeably, "heterocycle," as used herein, alone or in combination, each refer to a saturated, partially unsaturated, or fully unsaturated (but nonaromatic) monocyclic, bicyclic, or tricyclic heterocyclic group containing at least one heteroatom as a ring member, wherein each said heteroatom may be independently chosen from nitrogen, oxygen, and sulfur. In certain embodiments, said hetercycloalkyl will comprise from 1 to 4 heteroatoms as ring members. In further embodiments, said hetercycloalkyl will comprise from 1 to 2 heteroatoms as ring members. In certain embodiments, said hetercycloalkyl will comprise from 3 to 8 ring members in each ring. In further embodiments, said hetercycloalkyl will comprise from 3 to 7 ring members in each ring. In yet further embodiments, said hetercycloalkyl will comprise from 5 to 6 ring members in each ring. "Heterocycloalkyl" and "heterocycle" are intended to include sulfones, sulfoxides, N-oxides of tertiary nitrogen ring members, and carbocyclic fused and benzo fused ring systems; additionally, both terms also include systems where a heterocycle ring is fused to an aryl group, as defined herein, or an additional heterocycle group. Examples of heterocycle groups include tetrhydroisoquinoline, aziridinyl, azetidinyl, 1,3-benzodioxolyl, dihydroisoindolyl, dihydroisoquinolinyl, dihydrocinnolinyl, dihydrobenzodioxinyl, dihydro[1,3]oxazolo[4,5-b]pyridinyl, benzothiazolyl, dihydroindolyl, dihy-dropyridinyl, 1,3-dioxanyl, 1,4-dioxanyl, 1,3-dioxolanyl, isoindolinyl, morpholinyl, piperazinyl, pyrrolidinyl, tetrahydropyridinyl, piperidinyl, thiomorpholinyl, and the like. The heterocycle groups may be optionally substituted unless specifically prohibited.
  • The term "hydrazinyl" as used herein, alone or in combination, refers to two amino groups joined by a single bond, i.e., -N-N-.
  • The term "hydroxy," as used herein, alone or in combination, refers to -OH.
  • The term "hydroxyalkyl," as used herein, alone or in combination, refers to a hydroxy group attached to the parent molecular moiety through an alkyl group.
  • The term "imino," as used herein, alone or in combination, refers to =N-.
  • The term "iminohydroxy," as used herein, alone or in combination, refers to =N(OH) and =N-O-.
  • The phrase "in the main chain" refers to the longest contiguous or adjacent chain of carbon atoms starting at the point of attachment of a group to the compounds of any one of the formulas disclosed herein.
  • The term "isocyanate" refers to a -NCO group.
  • The term "isothiocyanato" refers to a -NCS group.
  • The phrase "linear chain of atoms" refers to the longest straight chain of atoms independently selected from carbon, nitrogen, oxygen and sulfur.
  • The term "lower," as used herein, alone or in a combination, where not otherwise specifically defined, means containing from 1 to and including 6 carbon atoms (i.e., C1-C6 alkyl).
  • The term "lower aryl," as used herein, alone or in combination, means phenyl or naphthyl, either of which may be optionally substituted as provided.
  • The term "lower heteroaryl," as used herein, alone or in combination, means either 1) monocyclic heteroaryl comprising five or six ring members, of which between one and four said members may be heteroatoms chosen from N, O, and S, or 2) bicyclic heteroaryl, wherein each of the fused rings comprises five or six ring members, comprising between them one to four heteroatoms chosen from N, O, and S.
  • The term "lower cycloalkyl," as used herein, alone or in combination, means a monocyclic cycloalkyl having between three and six ring members (i.e., C3-C6 cycloalkyl). Lower cycloalkyls may be unsaturated. Examples of lower cycloalkyl include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
  • The term "lower heterocycloalkyl," as used herein, alone or in combination, means a monocyclic heterocycloalkyl having between three and six ring members, of which between one and four may be heteroatoms chosen from N, O, and S (i.e., C3-C6 heterocycloalkyl). Examples of lower heterocycloalkyls include pyrrolidinyl, imidazolidinyl, pyrazolidinyl, piperidinyl, piperazinyl, and morpholinyl. Lower heterocycloalkyls may be unsaturated.
  • The term "lower amino," as used herein, alone or in combination, refers to -NRR', wherein R and R are independently chosen from hydrogen and lower alkyl, either of which may be optionally substituted.
  • The term "mercaptyl" as used herein, alone or in combination, refers to an RS- group, where R is as defined herein.
  • The term "nitro," as used herein, alone or in combination, refers to -NO2.
  • The terms "oxy" or "oxa," as used herein, alone or in combination, refer to -O-.
  • The term "oxo," as used herein, alone or in combination, refers to =O.
  • The term "perhaloalkoxy" refers to an alkoxy group where all of the hydrogen atoms are replaced by halogen atoms.
  • The term "perhaloalkyl" as used herein, alone or in combination, refers to an alkyl group where all of the hydrogen atoms are replaced by halogen atoms.
  • The terms "sulfonate," "sulfonic acid," and "sulfonic," as used herein, alone or in combination, refer the -SO3H group and its anion as the sulfonic acid is used in salt formation.
  • The term "sulfanyl," as used herein, alone or in combination, refers to -S-.
  • The term "sulfinyl," as used herein, alone or in combination, refers to -S(O)-.
  • The term "sulfonyl," as used herein, alone or in combination, refers to -S(O)2-.
  • The term "N-sulfonamido" refers to a RS(=O)2NR'- group with R and R' as defined herein.
  • The term "S-sulfonamido" refers to a -S(=O)2NRR', group, with R and R' as defined herein.
  • The terms "thia" and "thio," as used herein, alone or in combination, refer to a -S- group or an ether wherein the oxygen is replaced with sulfur. The oxidized derivatives of the thio group, namely sulfinyl and sulfonyl, are included in the definition of thia and thio.
  • The term "thiol," as used herein, alone or in combination, refers to an -SH group.
  • The term "thiocarbonyl," as used herein, when alone includes thioformyl -e(S)H and in combination is a -e(S)- group.
  • The term "N-thiocarbamyl" refers to an ROC(S)NR'- group, with R and R'as defined herein.
  • The term "O-thiocarbamyl" refers to a -OC(S)NRR', group with R and R'as defined herein.
  • The term "thiocyanato" refers to a -CNS group.
  • The term "trihalomethanesulfonamido" refers to a X3CS(O)2NR- group with X is a halogen and R as defined herein.
  • The term "trihalomethanesulfonyl" refers to a X3CS(O)2- group where X is a halogen.
  • The term "trihalomethoxy" refers to a X3CO- group where X is a halogen.
  • The term "trisubstituted silyl," as used herein, alone or in combination, refers to a silicone group substituted at its three free valences with groups as listed herein under the definition of substituted amino. Examples include trimethysilyl, tert-butyldimethylsilyl, triphenylsilyl and the like.
  • Any definition herein may be used in combination with any other definition to describe a composite structural group. By convention, the trailing element of any such definition is that which attaches to the parent moiety. For example, the composite group alkylamido would represent an alkyl group attached to the parent molecule through an amido group, and the term alkoxyalkyl would represent an alkoxy group attached to the parent molecule through an alkyl group.
  • When a group is defined to be "null," what is meant is that said group is absent.
  • The term "optionally substituted" means the anteceding group may be substituted or unsubstituted. When substituted, the substituents of an "optionally substituted" group may include, without limitation, one or more substituents independently selected from the following groups or a particular designated set of groups, alone or in combination: lower alkyl, lower alkenyl, lower alkynyl, lower alkanoyl, lower heteroalkyl, lower heterocycloalkyl, lower haloalkyl, lower haloalkenyl, lower haloalkynyl, lower perhaloalkyl, lower perhaloalkoxy, lower cycloalkyl, phenyl, aryl, aryloxy, lower alkoxy, lower haloalkoxy, oxo, lower acyloxy, carbonyl, carboxyl, lower alkylcarbonyl, lower carboxyester, lower carboxamido, cyano, hydrogen, halogen, hydroxy, amino, lower alkylamino, arylamino, amido, nitro, thiol, lower alkylthio, lower haloalkylthio, lower perhaloalkylthio, arylthio, sulfonate, sulfonic acid, trisubstituted silyl, N3, SH, SCH3, C(O)CH3, CO2CH3, CO2H, pyridinyl, thiophene, furanyl, lower carbamate, and lower urea. Where structurally feasible, two substituents may be joined together to form a fused five-, six-, or sevenmembered carbocyclic or heterocyclic ring consisting of zero to three heteroatoms, for example forming methylenedioxy or ethylenedioxy. An optionally substituted group may be unsubstituted (e.g., -CH2CH3), fully substituted (e.g., -CF2CF3), monosubstituted (e.g., -CH2CH2F) or substituted at a level anywhere inbetween fully substituted and monosubstituted (e.g., -CH2CF3). Where substituents are recited without qualification as to substitution, both substituted and unsubstituted forms are encompassed. Where a substituent is qualified as "substituted," the substituted form is specifically intended. Additionally, different sets of optional substituents to a particular moiety may be defined as needed; in these cases, the optional substitution will be as defined, often immediately following the phrase, "optionally substituted with."
  • As used herein, a substituted group is derived from the unsubstituted parent group in which there has been an exchange of one or more hydrogen atoms for another atom or group. Unless otherwise indicated, when a group is deemed to be "substituted," it is meant that the group is substituted with one or more substituents independently selected from C1-C6 alkyl, C1-C6 alkenyl, C1-C6 alkynyl, C1-C6 heteroalkyl, C3-C7 carbocyclyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), C3-C7-carbocyclyl-C1-C6-alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 3-10 membered heterocyclyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 3-10 membered heterocyclyl-C1-C6-alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), aryl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), aryl(C1-C6)alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 5-10 membered heteroaryl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 5-10 membered heteroaryl(C1-C6)alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), halo, cyano, hydroxy, C1-C6 alkoxy, C1-C6 alkoxy(C1-C6)alkyl (i.e., ether), aryloxy, sulfhydryl (mercapto), halo(C1-C6)alkyl (e.g., -CF3), halo(C1-C6)alkoxy (e.g., -OCF3), C1-C6 alkylthio, arylthio, amino, amino(C1-C6)alkyl, nitro, O-carbamyl, N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, O-carboxy, acyl, cyanato, isocyanato, thiocyanato, isothiocyanato, sulfinyl, sulfonyl, and oxo (=O). Wherever a group is described as "optionally substituted" that group can be substituted with the above substituents.
  • The term R or the term R', appearing by itself and without a number designation, unless otherwise defined, refers to a moiety chosen from hydrogen, alkyl, cycloalkyl, heteroalkyl, aryl, heteroaryl and heterocycloalkyl, any of which may be optionally substituted. Such R and R' groups should be understood to be optionally substituted as defined herein. Whether an R group has a number designation or not, every R group, including R, R' and Rn where n=(1, 2, 3, ...n), every substituent, and every term should be understood to be independent of every other in terms of selection from a group. Should any variable, substituent, or term (e.g. aryl, heterocycle, R, etc.) occur more than one time in a formula or generic structure, its definition at each occurrence is independent of the definition at every other occurrence. Those of skill in the art will further recognize that certain groups may be attached to a parent molecule or may occupy a position in a chain of elements from either end as written. For example, an unsymmetrical group such as -C(O)N(R)- may be attached to the parent moiety at either the carbon or the nitrogen.
  • Asymmetric centers exist in the compounds disclosed herein. These centers are designated by the symbols "R" or "S," depending on the configuration of substituents around the chiral carbon atom. It should be understood that the disclosure encompasses all stereochemical isomeric forms, including diastereomeric, enantiomeric, and epimeric forms,as well as d-isomers and 1-isomers, and mixtures thereof. Individual stereoisomers of compounds can be prepared synthetically from commercially available starting materials which contain chiral centers or by preparation of mixtures of enantiomeric products followed by separation such as conversion to a mixture of diastereomers followed by separation or recrystallization, chromatographic techniques, direct separation of enantiomers on chiral chromatographic columns, or any other appropriate method known in the art. Starting compounds of particular stereochemistry are either commercially available or can be made and resolved by techniques known in the art. Additionally, the compounds disclosed herein may exist as geometric isomers. The present disclosure includes all cis, trans, syn, anti, entgegen (E), and zusammen (Z) isomers as well as the appropriate mixtures thereof. Additionally, compounds may exist as tautomers; all tautomeric isomers are provided by this disclosure. Additionally, the compounds disclosed herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. In general, the solvated forms are considered equivalent to the unsolvated forms.
  • The term "bond" refers to a covalent linkage between two atoms, or two moieties when the atoms joined by the bond are considered to be part of larger substructure. A bond may be single, double, or triple unless otherwise specified. A dashed line between two atoms in a drawing of a molecule indicates that an additional bond may be present or absent at that position.
  • The term "disease" as used herein is intended to be generally synonymous, and is used interchangeably with, the terms "disorder," "syndrome," and "condition" (as in medical condition), in that all reflect an abnormal condition of the human or animal body or of one of its parts that impairs normal functioning, is typically manifested by distinguishing signs and symptoms, and causes the human or animal to have a reduced duration or quality of life.
  • The term "combination therapy" means the administration of two or more therapeutic agents to treat a therapeutic condition or disorder described in the present disclosure. Such administration encompasses coadministration of these therapeutic agents in a substantially simultaneous manner, such as in a single capsule having a fixed ratio of active ingredients or in multiple, separate capsules for each active ingredient. In addition, such administration also encompasses use of each type of therapeutic agent in a sequential manner. In either case, the treatment regimen will provide beneficial effects of the drug combination in treating the conditions or disorders described herein.
  • The phrase "therapeutically effective" is intended to qualify the amount of active ingredients used in the treatment of a disease or disorder or on the effecting of a clinical endpoint.
  • The term "therapeutically acceptable" refers to those compounds (or salts, prodrugs, tautomers, zwitterionic forms, etc.) which are suitable for use in contact with the tissues of patients without undue toxicity, irritation, and allergic response, are commensurate with a reasonable benefit/risk ratio, and are effective for their intended use.
  • As used herein, reference to "treatment" of a patient is intended to include prophylaxis. Treatment may also be preemptive in nature, i.e., it may include prevention of disease. Prevention of a disease may involve complete protection from disease, for example as in the case of prevention of infection with a pathogen, or may involve prevention of disease progression. For example, prevention of a disease may not mean complete foreclosure of any effect related to the diseases at any level, but instead may mean prevention of the symptoms of a disease to a clinically significant or detectable level. Prevention of diseases may also mean prevention of progression of a disease to a later stage of the disease.
  • The term "patient" is generally synonymous with the term "subject" and includes all mammals including humans. Examples of patients include humans, livestock such as cows, goats, sheep, pigs, and rabbits, and companion animals such as dogs, cats, rabbits, and horses. Preferably, the patient is a human.
  • The term "prodrug" refers to a compound that is made more active in vivo. Certain compounds disclosed herein may also exist as prodrugs, as described in Hydrolysis in Drug and Prodrug Metabolism : Chemistry, Biochemistry, and Enzymology (Testa, Bernard and Mayer, Joachim M. Wiley-VHCA, Zurich, Switzerland 2003). Prodrugs of the compounds described herein are structurally modified forms of the compound that readily undergo chemical changes under physiological conditions to provide the compound. Additionally, prodrugs can be converted to the compound by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to a compound when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent. Prodrugs are often useful because, in some situations, they may be easier to administer than the compound, or parent drug. They may, for instance, be bioavailable by oral administration whereas the parent drug is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug. A wide variety of prodrug derivatives are known in the art, such as those that rely on hydrolytic cleavage or oxidative activation of the prodrug. An example, without limitation, of a prodrug would be a compound which is administered as an ester (the "prodrug"), but then is metabolically hydrolyzed to the carboxylic acid, the active entity. Additional examples include peptidyl derivatives of a compound.
  • The compounds disclosed herein can exist as therapeutically acceptable salts. The present disclosure includes compounds listed above in the form of salts, including acid addition salts. Suitable salts include those formed with both organic and inorganic acids. Such acid addition salts will normally be pharmaceutically acceptable. However, salts of non-pharmaceutically acceptable salts may be of utility in the preparation and purification of the compound in question. Basic addition salts may also be formed and be pharmaceutically acceptable. For a more complete discussion of the preparation and selection of salts, refer to Pharmaceutical Salts: Properties, Selection, and Use (Stahl, P. Heinrich. Wiley-VCHA, Zurich, Switzerland, 2002).
  • Basic addition salts can be prepared during the final isolation and purification of the compounds by reacting a carboxy group with a suitable base such as the hydroxide, carbonate, or bicarbonate of a metal cation or with ammonia or an organic primary, secondary, or tertiary amine. The cations of therapeutically acceptable salts include lithium, sodium, potassium, calcium, magnesium, and aluminum, as well as nontoxic quaternary amine cations such as ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, diethylamine, ethylamine, tributylamine, pyridine, N,N-dimethylaniline, N-methylpiperidine, N-methylmorpholine, dicyclohexylamine, procaine, dibenzylamine, N,N-dibenzylphenethylamine, 1-ephenamine, and N,N'-dibenzylethylenediamine. Other representative organic amines useful for the formation of base addition salts include ethylenediamine, ethanolamine, diethanolamine, piperidine, and piperazine.
  • Other carrier materials and modes of administration known in the pharmaceutical art may also be used. Pharmaceutical compositions of the disclosure may be prepared by any of the well-known techniques of pharmacy, such as effective formulation and administration procedures. Preferred unit dosage formulations are those containing an effective dose, as herein below recited, or an appropriate fraction thereof, of the active ingredient.
  • It should be understood that in addition to the ingredients particularly mentioned above, the formulations described above may include other agents conventional in the art having regard to the type of formulation in question, for example those suitable for oral administration may include flavoring agents.
  • The amount of active ingredient that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration.
  • The compounds can be administered in various modes, e.g. orally, topically, or by injection. The precise amount of compound administered to a patient will be the responsibility of the attendant physician. The specific dose level for any particular patient will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diets, time of administration, route of administration, rate of excretion, drug combination, the precise disorder being treated, and the severity of the indication or condition being treated. In addition, the route of administration may vary depending on the condition and its severity. The above considerations concerning effective formulations and administration procedures are well known in the art and are described in standard textbooks.
    • Combinations and Combination Therapy
  • ln certain instances, it may be appropriate to administer at least one of the compounds described herein (or a pharmaceutically acceptable salt thereof) in combination with another therapeutic agent. By way of example only, if one of the side effects experienced by a patient upon receiving one of the compounds herein is hypertension, then it may be appropriate to administer an anti-hypertensive agent in combination with the initial therapeutic agent. Or, by way of example only, the therapeutic effectiveness of one of the compounds described herein may be enhanced by administration of an adjuvant (i.e., by itself the adjuvant may only have minimal therapeutic benefit, but in combination with another therapeutic agent, the overall therapeutic benefit to the patient is enhanced). Or, by way of example only, the benefit of experienced by a patient may be increased by administering one of the compounds described herein with another therapeutic agent (which also includes a therapeutic regimen) that also has therapeutic benefit. By way of example only, in a treatment for diabetes involving administration of one of the compounds described herein, increased therapeutic benefit may result by also providing the patient with another therapeutic agent for diabetes. In any case, regardless of the disease, disorder or condition being treated, the overall benefit experienced by the patient may simply be additive of the two therapeutic agents or the patient may experience a synergistic benefit.
  • Specific, non-limiting examples of possible combination therapies include use of certain compounds of the disclosure with an ACE inhibitor.
  • In any case, the multiple therapeutic agents (at least one of which is a compound disclosed herein) may be administered in any order or even simultaneously. If simultaneously, the multiple therapeutic agents may be provided in a single, unified form, or in multiple forms (by way of example only, either as a single pill or as two separate pills). One of the therapeutic agents may be given in multiple doses, or both may be given as multiple doses. If not simultaneous, the timing between the multiple doses may be any duration of time ranging from a few minutes to four weeks.
  • Thus, in another aspect, certain embodiments provide methods for treating fxn-mediated disorders in a human or animal subject in need of such treatment comprising administering to said subject an amount of a compound disclosed herein effective to reduce or prevent said disorder in the subject, in combination with at least one additional agent for the treatment of said disorder that is known in the art. In a related aspect, certain embodiments provide therapeutic compositions comprising at least one compound disclosed herein in combination with one or more additional agents for the treatment of fxn-mediated disorders.
  • Besides being useful for human treatment, certain compounds and formulations disclosed herein may also be useful for veterinary treatment of companion animals, exotic animals and farm animals, including mammals, rodents, and the like. More preferred animals include horses, dogs, and cats.
    • Compound Synthesis
  • Compounds of the present disclosure can be prepared using methods illustrated in general synthetic schemes and experimental procedures detailed below. General synthetic schemes and experimental procedures are presented for purposes of illustration and are not intended to be limiting. Starting materials used to prepare compounds of the present disclosure are commercially available or can be prepared using routine methods known in the art.
    • List of Abbreviations
  • Ac2O = acetic anhydride; AcCl = acetyl chloride; AcOH = acetic acid; AIBN = azobisisobutyronitrile; aq. = aqueous; Bu3SnH = tributyltin hydride; CD3OD = deuterated methanol; CDCl3 = deuterated chloroform; CDI = 1,1'-Carbonyldiimidazole; DBU = 1,8-diazabicyclo[5.4.0]undec-7-ene; DCM = dichloromethane; DEAD = diethyl azodicarboxylate; DIBAL-H = di-iso-butyl aluminium hydride; DIEA = DIPEA = N,N-diisopropylethylamine; DMAP = 4-dimethylaminopyridine; DMF = N,N-dimethylformamide; DMSO-d6 = deuterated dimethyl sulfoxide; DMSO = dimethyl sulfoxide; DPPA = diphenylphosphoryl azide; EDC.HCl = EDCI.HCl = 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride; Et2O = diethyl ether; EtOAc = ethyl acetate; EtOH = ethanol; h = hour; HATU=2-(1H-7-azabenzotriazol-1-yl)-1,1,3,3-tetramethyl uronium hexafluorophosphate methanaminium; HMDS = hexamethyldisilazane; HOBT = 1-hydroxybenzotriazole; i-PrOH = isopropanol; LAH = lithium aluminium hydride; LiHMDS = Lithium bis(trimethylsilyl)amide; MeCN = acetonitrile; MeOH = methanol; MP-carbonate resin = macroporous triethylammonium methylpolystyrene carbonate resin; MsCI = mesyl chloride; MTBE = methyl tertiary butyl ether; MW = microwave irradiation ; n-BuLi = n-butyllithium; NaHMDS = Sodium bis(trimethylsilyl)amide; NaOMe = sodium methoxide; NaOtBu = sodium t-butoxide; NBS = N-bromosuccinimide; NCS = N-chlorosuccinimide; NMP = N-Methyl-2-pyrrolidone; Pd(Ph3)4 = tetrakis(triphenylphosphine)palladium(0); Pd2(dba)3 = tris(dibenzylideneacetone)dipalladium(0); PdCl2(PPh3)2 = bis(triphenylphosphine)palladium(II) dichloride; PG = protecting group; prep-HPLC = preparative high-performance liquid chromatography; PyBop = (benzotriazol-1-yloxy)-tripyrrolidinophosphonium hexafluorophosphate; Pyr = pyridine; RT = room temperature; RuPhos = 2-dicyclohexylphosphino-2',6'-diisopropoxybiphenyl; sat. = saturated; ss = saturated solution; t-BuOH = tert-butanol; T3P = Propylphosphonic Anhydride; TBS = TBDMS = tert-butyldimethylsilyl; TBSCl = TBDMSCl = tert-butyldimethylchlorosilane; TEA = Et3N = triethylamine; TFA = trifluoroacetic acid; TFAA = trifluoroacetic anhydride; THF = tetrahydrofuran; Tol = toluene; TsCl = tosyl chloride; XPhos = 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl.
    • General Synthetic Methods for Preparing Compounds
  • In general, polyamides of the present disclosure may be synthesized by solid supported synthetic methods, using compounds such as Boc-protected straight chain aliphatic and heteroaromatic amino acids, and alkylated derivatives thereof, which are cleaved from the support by aminolysis, deprotected (e.g., with sodium thiophenoxide), and purified by reverse-phase HPLC, as well known in the art. The identity and purity of the polyamides may be verified using any of a variety of analytical techniques available to one skilled in the art such as 1H-NMR, analytical HPLC, or mass spectrometry.
  • The following scheme can be used to practice the present disclosure.
    Figure imgb0364
  • The compounds disclosed herein can be synthesized using Scheme I. For clarity and compactness, the scheme depicts the synthesis of a diamide comprising subunits "C" and "D", both of which are represented as unspecified five-membered rings having amino and carboxy moieties. The amino group of subunit "D" is protected with a protecting group "PG" such as a Boc or CBz carbamate to give 101. The free )carboxylic acid is then reacted with a solid support, using a coupling reagent such as EDC, to give the supported compound 103. Removal of PG under acidic conditions gives the free amine 104, which is coupled with the nitrogen-protected carboxylic acid 105 to give amide 106. Removal of PG under acidic conditions gives the free amine 107. In this example, the free amine is reacted with acetic anhydride to form an acetamide (not shown. The molecule is then cleaved from the solid support under basic conditions to give carboxylic acid 108. Methods for attachment of the linker L and recruiting moiety X are disclosed below.
  • The person of skill will appreciate that many variations of the above scheme are available to provide a wide range of compounds:
    1) The sequence 104 -106 -107 can be repeated as often as desired, in order to form longer polyamine sequences.
    2) A variety of amino heterocycle carboxylic acids can be used, to form different subunits. Table 3, while not intended to be limiting, provides several heterocycle amino acids that are contemplated for the synthesis of the compounds in this disclosure. Carbamate protecting groups PG can be incorporated using techniques that are well established in the art. Table 3. Heterocyclic amino acids.
    Structure
    Figure imgb0365
    Figure imgb0366
    Figure imgb0367
    Figure imgb0368
    Figure imgb0369
    Figure imgb0370
    Figure imgb0371
    Figure imgb0372
    Figure imgb0373
    Figure imgb0374
    Figure imgb0375
    Figure imgb0376
    Figure imgb0377
     (Z is H, C1-6 alkyl, amine, or halogen)
    Figure imgb0378
     (Z is H, C1-6 alkyl, amine, or halogen)
    Figure imgb0379
    Figure imgb0380
    Figure imgb0381
    Figure imgb0382
    Figure imgb0383
    Figure imgb0384
    Figure imgb0385
    Figure imgb0386
    Figure imgb0387
    3) Hydroxy-containing heterocyclic amino acids can be incorporated into Scheme I as their TBS ethers. While not intended to be limiting, Scheme II provides the synthesis of TBS-protected heterocyclic amino acids contemplated for the synthesis of the compounds in this disclosure.
    Figure imgb0388
     4) Aliphatic amino acids can be used in the above synthesis for the formation of spacer units "W" and subunits for recognition of DNA nucleotides. Table 4, while not intended to be limiting, provides several aliphatic amino acids contemplated for the synthesis of the compounds in this disclosure. Table 4. Aliphatic amino acids.
    Structure
    Figure imgb0389
     beta-alanine (β)
    Figure imgb0390
     gamma-aminobutyric acid ("gAB" or γ)
    Figure imgb0391
     3-(2-aminoethoxy)propanoic acid
    Figure imgb0392
     3-((2-aminoethyl)(2-oxo-2-phenyl-1λ2-ethyl)amino)propanoic acid
    Figure imgb0393
    Figure imgb0394
     (R is H, C1-6 alkyl)
    Figure imgb0395
     (R is H, C1-6 alkyl, aryl, or heteroaryl)
    Figure imgb0396
    Figure imgb0397
    Figure imgb0398
    Figure imgb0399
    Figure imgb0400
     X is F or OH
    Figure imgb0401
  • Attachment of the linker L and recruiting moiety X can be accomplished with the methods disclosed in Scheme III, which uses a triethylene glycol moiety for the linker L. The mono-TBS ether of triethylene glycol 301 is converted to the bromo compound 302 under Mitsunobu conditions. The recruiting moiety X is attached by displacement of the bromine with a hydroxyl moiety, affording ether 303. The TBS group is then removed by treatment with fluoride, to provide alcohol 304, which will be suitable for coupling with the polyamide moiety. Other methods will be apparent to the person of skill in the art for inclusion of alternate linkers L, including but not limited to propylene glycol or polyamine linkers, or alternate points of attachment of the recruiting moiety X, including but not limited to the use of amines and thiols.
    Figure imgb0402
  • Synthesis of the X-L-Y molecule can be completed with the methods set forth in Scheme IV. Carboxylic acid 108 is converted to the acid chloride 401. Reaction with the alcohol functionality of 301 under basic conditions provides the coupled product 402. Other methods will be apparent to the person of skill in the art for performing the coupling procedure, including but not limited to the use of carbodiimide reagents. For instance, the amide coupling reagents can be used, but not limited to, are carbodiimides such as dicyclohexylcarbodiimide (DCC), diisopropylcarbodiimide (DIC), ethyl-(N',N'-dimethylamino)propylcarbodiimide hydrochloride (EDC), in combination with reagents such as 1-hydroxybenzotriazole (HOBt), 4-(N,N-dimethylamino)pyridine (DMAP) and diisopropylethylamine (DIEA). Other reagents are also often used depending the actual coupling reactions are (Benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), (Benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate (PyBOP), (7-Azabenzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate (PyAOP), Bromotripyrrolidinophosphonium hexafluorophosphate (PyBrOP), Bis(2-oxo-3-oxazolidinyl)phosphinic chloride (BOP-Cl), O-(Benzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HBTU), O-(Benzotriazol-1-yl)- N,N,N',N'-tetramethyluronium tetrafluoroborate (TBTU), O-(7-Azabenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU), O-(7-Azabenzotriazol-1-yl)- N,N,N',N'-tetramethyluromum tetrafluoroborate (TATU), O-(6-Chlorobenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HCTU), Carbonyldiimidazole (CDI), and N,N,N',N'-Tetramethylchloroformamidinium Hexafluorophosphate (TCFH).
    Figure imgb0403
  • A proposed synthesis of a rohitukine-based CDK9 inhibitor is set forth in Scheme V. Synthesis begins with the natural product rohitukine, which is a naturally available compound that has been used as a precursor for CDK9-active drugs such as Alvocidib. The existing hydroxy groups are protected as TBS ethers, the methyl group is brominated, and the bromo compound is coupled with a suitably functionalized linker reagent such as 501 to afford the linked compound 502. Variants of this procedure will be apparent to the person of skill.
    Figure imgb0404
  • Proposed syntheses of DB08045-based cyclin T1 inhibitors are set forth in Scheme VI. Synthesis begins with DB08045, which contains a primary amino group that is available for functionalization. Coupling of the amino group with a carboxylic acid under conventional conditions gives amide 601. Alternatively, reductive amination with a carboxaldehyde gives amine 602. Variants of this procedure will be apparent to the person of skill.
    Figure imgb0405
  • A proposed synthesis of an A-395 based PRC2 inhibitor is set forth in Scheme VII. The piperidine compound 701, a precursor to A-395, can be reacted with methanesulfonyl chloride 702 to give A-395. In a variation of this synthesis, 701 is reacted with linked sulfonyl chloride 703, to provide linked A-395 inhibitor 704
    • Attaching protein binding molecules to oligomeric backbone
  • Generally the oligomeric backbone is functionalized to adapt to the type of chemical reactions can be performed to link the oligomers to the attaching position in protein binding moieties. The type reactions are suitable but not limited to, are amide coupling reactions, ether formation reactions (O-alkylation reactions), amine formation reactions (N-alkylation reactions), and sometimes carbon-carbon coupling reactions. The general reactions used to link oligomers and protein binders are shown in below schemes (VIII through X). The compounds and structures shown in Table 2 can be attached to the oligomeric backbone described herein at any position that is chemically feasible while not interfering with the hydrogen bond between the compound and the regulatory protein.
    Figure imgb0406
  • Either the oligomer or the protein binder can be functionalized to have a carboxylic acid and the other coupling counterpart being functionalized with an amino group so the moieties can be conjugated together mediated by amide coupling reagents. The amide coupling reagents can be used, but not limited to, are carbodiimides such as dicyclohexylcarbodiimide (DCC), diisopropylcarbodiimide (DIC), ethyl-(N',N'-dimethylamino)propylcarbodiimide hydrochloride (EDC), in combination with reagents such as 1-hydroxybenzotriazole (HOBt), 4-(N,N-dimethylamino)pyridine (DMAP) and diisopropylethylamine (DIEA). Other reagents are also often used depending the actual coupling reactions are (Benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), (Benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate (PyBOP), (7-Arabenzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate (PyAOP), Bromotripyrrolidinophosphonium hexafluorophosphate (PyBrOP), Bis(2-oxo-3-oxazolidinyl)phosphinic chloride (BOP-Cl), O-(Benzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HBTU), O-(Benzotriazol-1-yl)- N,N,N',N'-tetramethyluronium tetrafluoroborate (TBTU), O-(7-Azabenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU), O-(7-Azabenzotriazol-1-yl)- N,N,N',N'-tetramethyluronium tetrafluoroborate (TATU), O-(6-Chlorobenzotriazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HCTU), Carbonyldiimidazole (CDI), and N,N,N',N'-Tetramethylchloroformamidinium Hexafluorophosphate (TCFH).
    Figure imgb0407
  • In an ether formation reaction, either the oligomer or the protein binder can be functionalized to have an hydroxyl group (phenol or alcohol) and the other coupling counterpart being functionalized with a leaving group such as halide, tosylate and mesylate so the moieties can be conjugated together mediated by a base or catalyst. The bases can be selected from, but not limited to, sodium hydride, potassium hydride, sodium hydroxide, potassium hydroxide, sodium carbonate, potassium carbonate. The catalyst can be selected from silver oxide, phase transfer reagents, iodide salts, and crown ethers.
    Figure imgb0408
  • In an N-alkylation reaction, either the oligomer or the protein binder can be functionalized to have an amino group (arylamine or alkylamine) and the other coupling counterpart being functionalized with a leaving group such as halide, tosylate and mesylate so the moieties can be conjugated together directly or with a base or catalyst. The bases can be selected from, but not limited to, sodium hydride, potassium hydride, sodium hydroxide, potassium hydroxide, sodium carbonate, potassium carbonate. The catalyst can be selected from silver oxide, phase transfer reagents, iodide salts, and crown ethers. The alkylation of amines can also be achieved through reductive amination reactions, where in either the oligomer or the protein binder can be functionalized to have an amino group (arylamine or alkylamine) and the other coupling counterpart being functionalized with an aldehyde or ketone group so the moieties can be conjugated together with the treatment of a reducing reagent (hydride source) directly or in combination with a dehydration agent. The reducing reagents can be selected from, but not limited to, NaBH4, NaHB(OAc)3, NaBH3CN, and dehydration agents are normally Ti(iPrO)4, Ti(OEt)4, Al(iPrO)3, orthoformates and activated molecular sieves.
    • Cell-penetrating ligand
  • In one aspect, the compounds of the present disclosure comprises a cell-penetrating ligand moiety. The cell-penetrating ligand moiety serves to facilitate transport of the compound across cell membranes. In certain embodiments, the cell-penetrating ligand moiety is a polypeptide. Several peptide sequences can facilitate passage into the cell, including polycationic sequences such as poly-R; arginine-rich sequences interspersed with spacers such as (RXR)n (X = 6-aminohexanoic acid) and (RXRRBR)n (B = beta-alanine); sequences derived from the Penetratin peptide; and sequences derived from the PNA/PMO internalisation peptide (Pip). The Pip5 series is characterized by the sequence ILFQY.
  • In certain embodiments, the cell-penetrating polypeptide comprises an N-terminal cationic sequence H2N-(R)n-CO-, with n = 5-10, inclusive. In certain embodiments, the N-terminal cationic sequence contains 1, 2, or 3 substitutions of R for amino acid resides independently chosen from beta-alanine and 6-aminohexanoic acid.
  • In certain embodiments, the cell-penetrating polypeptide comprises the ILFQY sequence. In certain embodiments, the cell-penetrating polypeptide comprises the QFLY sequence. In certain embodiments, the cell-penetrating polypeptide comprises the QFL sequence.
  • In certain embodiments, the cell-penetrating polypeptide comprises a C-terminal cationic sequence - HN-(R)n-COOH, with n = 5-10, inclusive. In certain embodiments, the C-terminal cationic sequence contains 1, 2, or 3 substitutions of R for amino acid resides independently chosen from beta-alanine and 6-aminohexanoic acid. In certain embodiments, the C-terminal cationic sequence is substituted at every other position with an amino acid residue independently chosen from beta-alanine and 6-aminohexanoic acid. In certain embodiments, the C-terminal cationic sequence is -HN-RXRBRXRB-COOH. Table 5. Cell-penetrating peptides
    SEQ ID NO. Sequence
    SEQ ID NO. 1 GRKKRRQRRRPPQ
    SEQ ID NO. 2 RQIKIWFQNRRMKWKK
    SEQ ID NO. 3 KLALKLALKALKAALKLA
    SEQ ID NO. 4 GWTLNS/AGYLLGKINLKALAALAKKIL
    SEQ ID NO. 5 NAKTRRHERRRKLAIER
    SEQ ID NO. 6 RRRRRRRR
    SEQ ID NO. 7 RRRRRRRRR
    SEQ ID NO. 8 GALFLGFLGAAGSTMGA
    SEQ ID NO. 9 KETWWETWWTEWSQPKKKRKV
    SEQ ID NO. 10 LLIILRRRIRKQAHAHSK
    SEQ ID NO. 11 YTAIAWVKAFIRKLRK
    SEQ ID NO. 12 IAWVKAFIRKLRKGPLG
    SEQ ID NO. 13 MVTVLFRRLRIRRACGPPRVRV
    SEQ ID NO. 14 GLWRALWRLLRSLWRLLWRA
    SEQ ID NO. 15 RRRRRRR QIKIWFQNRRMKWKKGG
    SEQ ID NO. 16 RXRRXRRXRIKILFQNRRMKWKK
    SEQ ID NO. 17 RXRRXRRXRIdKILFQNdRRMKWHKB
    SEQ ID NO. 18 RXRRXRRXRIHILFQNdRRMKWHKB
    SEQ ID NO. 19 RXRRBRRXRILFQYRXRBRXRB
    SEQ ID NO. 20 RXRRBRRXRILFQYRXRXRXRB
    SEQ ID NO. 21 RXRRXRILFQYRXRRXR
    SEQ ID NO. 22 RBRRXRRBRILFQYRBRXRBRB
    SEQ ID NO. 23 RBRRXRRBRILFQYRXRBRXRB
    SEQ ID NO. 24 RBRRXRRBRILFQYRXRRXRB
    SEQ ID NO. 25 RBRRXRRBRILFQYRXRBRXB
    SEQ ID NO. 26 RXRRBRRXRILFQYRXRRXRB
    SEQ ID NO. 27 RXRRBRRXRILFQYRXRBRXB
    SEQ ID NO. 28 RXRRBRRXRYQFLIRXRBRXRB
    SEQ ID NO. 29 RXRRBRRXRIQFLIRXRBRXRB
    SEQ ID NO. 30 RXRRBRRXRQFLIRXRBRXRB
    SEQ ID NO. 31 RXRRBRRXRQFLRXRBRXRB
    SEQ ID NO. 32 RXRRBRRXYRFLIRXRBRXRB
    SEQ ID NO. 33 RXRRBRRXRFQILYRXRBRXRB
    SEQ ID NO. 34 RXRRBRRXYRFRLIXRBRXRB
    SEQ ID NO. 35 RXRRBRRXILFRYRXRBRXRB
    SEQ ID NO. 36 Ac-RRLSYSRRRFXBpgG
    SEQ ID NO. 37 Ac-RRLSYSRRRFPFVYLIXBpgG
    Ac = acetyl; Bpg = L-bis-homopropargylglycine =
    Figure imgb0409
     B = beta-alanine; X = 6-aminohexanoic acid; dK/dR = corresponding D-amino acid.
    • EXAMPLES
  • The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.
  • While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments described herein may be employed. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
    • Example 1.
  • Scheme A describes the steps involved for preparing the polyamide, attaching the polyamide to the oligomeric backbone, and then attaching the ligand to the other end of the oligomeric backbone. The second terminus can include any structure in Table 2. The oligomeric backbone can be selected from the various combinations of linkers shown in Table 6. The transcription modulator molecule such as those listed in Table 7 below can be prepared using the synthesis scheme shown below. Table 6. Examples of oligomeric backbone as represented by -(T1-V1)a-(T2-V2)b-(T3-V3)c-(T4-V4)d-(T5-V5)e-
    T1 V1 T2 V2 T3 V3 T4 V4 T5 V5
    (alkylene CONR1a (EA)w CO (PEG)n NR11CO ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O arylene NR11CO ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O Subst. arylene NR11CO ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O NR11C O (C1-C12) alkyl Subst. arylene NR11CO
    (C1-C12) alkylene CONR1a (EA)w CO (C1-C12) alkyl NR11CO-C1-4 alkyl Subst. arylene NR11 ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O Subst. arylene ---- ---- ----
    (PEG)n CONR1a- C1-4 alkyl ---- ---- ---- ---- ---- ---- ---- ----
    (EA)w CO (C1-C12) alkyl CONR11- C1-4 alkyl ---- ---- ---- ----- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n NR11CO-C1-4 alkyl ---- ---- ---- -----
    (EA)w CO (PEG)n O phenyl NR11CO-C1-4 alkyl ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (PEG)n CO ---- ---- ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO modifd. (PEG)n O arylene NR11CO ---- ----
    Table 7. Examples of transcription modulator molecules
    First terminus Oligomeric backbone Second terminus
    Im-β-Py
    Figure imgb0410
    Figure imgb0411
     (CBP binder)
    Im-β-Py
    Figure imgb0412
    Figure imgb0413
     (CBP binder)
    Im-β-Py
    Figure imgb0414
    Figure imgb0415
     (CBP binder)
    Im-β-Py
    Figure imgb0416
    Figure imgb0417
     (OGT binder)
    Im-β-Py
    Figure imgb0418
    Figure imgb0419
     (OGT binder)
    Im-β-Py
    Figure imgb0420
    Figure imgb0421
     (OGT binder)
    Im-β-Py
    Figure imgb0422
    Figure imgb0423
     (methyl lysine binder)
    Im-β-Py
    Figure imgb0424
    Figure imgb0425
     (methyl lysine binder)
    Im-β-Py
    Figure imgb0426
    Figure imgb0427
     (methyl lysine binder)
    Im-Py-β-gAB-Py-P-Py
    Figure imgb0428
    Figure imgb0429
     (CDK 1, 2, 5)
    Im-Py-β-gAB-Py-β-Py
    Figure imgb0430
    Figure imgb0431
     (CDK 1, 2, 5)
    Im-Py-β-gAB-Py-P-Py
    Figure imgb0432
    Figure imgb0433
     (CDK 1, 2, 5)
    Im-Py-β-gAB-Py-β-Py
    Figure imgb0434
    Figure imgb0435
     (methyl transferase)
    Im-Py-β-gAB-Py-P-Py
    Figure imgb0436
    Figure imgb0437
     (methyl transferase)
    Im-Py-β-gAB-Py-β-Py
    Figure imgb0438
    Figure imgb0439
     (methyl transferase)
    Im-Py-β-gAB-Py-β-Py
    Figure imgb0440
    Figure imgb0441
     (CBP binder)
    Im-Py-β-gAB-Py-β-Py
    Figure imgb0442
    Figure imgb0443
     (CBP binder)
    Im-Py-β-gAB-Py-β-Py
    Figure imgb0444
    Figure imgb0445
     (CBP binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0446
    Figure imgb0447
     (OGT binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0448
    Figure imgb0449
     (OGT binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0450
    Figure imgb0451
     (OGT binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0452
    Figure imgb0453
     (methyl lysine binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0454
    Figure imgb0455
     (methyl lysine binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0456
    Figure imgb0457
     (methyl lysine binder)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0458
    Figure imgb0459
     (CDK 1, 2, 5)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0460
    Figure imgb0461
     (CDK 1, 2, 5)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0462
    Figure imgb0463
     (CDK 1, 2, 5)
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0464
    Figure imgb0465
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0466
    Figure imgb0467
    Im-Py-Py-Im (Linked in the middle - either position 2 or 3) to Py-Py-Py-Py
    Figure imgb0468
    Figure imgb0469
    Figure imgb0470
  • The ligand or protein binder can be attached to the oligomeric backbone using the schemes described below. The oligomeric backbone can be linked to the protein binder at any position on the protein binder that is chemically feasible while not interfering with the binding between the protein binder and the regulatory protein. The protein binder binds to the regulatory protein often through hydrogen bonds, and linking the oligomeric backbone and the regulatory protein should not interfere the hydrogen bond formation. The protein binder is attached to the oligomeric backbone through an amide or ether bond. Scheme B through Scheme D demonstrate several examples of linking the oligomeric backbone and protein binder.
    Figure imgb0471
    Figure imgb0472
    Figure imgb0473
    Figure imgb0474
    • Example 2. Biological Activity Assays
  • The methods as set forth below will be used to demonstrate the binding of the disclosed compounds and the efficacy in treatment. In general, the assays are directed at evaluating the effect of the disclosed compounds on the level of expression of fxn.
    • Gene expression
  • Expression of fxnwill be assayed by techniques known in the field. These assays include, but are not limited to quantitative reverse transcription polymerase chain reaction (RT-PCR), microarray, or multiplexed RNA sequencing (RNA-seq), with the chosen assay measuring either total expression, or the allele specific expression of the fmr gene. Exemplary assays are found at: Freeman WM et al., "Quantitative RT-PCR: pitfalls and potential", BioTechniques 1999, 26, 112-125; Dudley AM et al, "Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range", PNAS USA 2002, 99(11), 7554-7559; Wang Z et al., "RNA-Seq: a revolutionary tool for transcriptomics" Nature Rev. Genetics 2009, 10, 57-63.
  • Production of the FMRP protein will be assayed by techniques known in the field. These assays include, but are not limited to Western blot assay, with the chosen assay measuring either total protein expression, or allele specific expression of the fmr gene.
  • For use in assay, two tissue models and two animal models are contemplated.
    • Disease Model I: Human cell culture
  • This model will constitute patient-derived cells, including fibroblasts, induced pluripotent stem cells and cells differentiated from stem cells. Attention will be made in particular to cell types that show impacts of the disease, e.g., neuronal cell types.
    • Disease Model II: Murine cell culture
  • This model will constitute cell cultures from mice from tissues that are particularly responsible for disease symptoms, which will include fibroblasts, induced pluripotent stem cells and cells differentiated from stem cells and primary cells that show impacts of the disease, e.g., neuronal cell types.
    • Disease Model III: Murine
  • This model wil constitute mice whose genotypes contain the relevant number of repeats for the disease phenotype - these models should show the expected altered gene expression (e.g., a variation in fxnexpression).
    • Disease Model IV: Murine
  • This model will constitute mice whose genotypes contain a knock in of the human genetic locus from a diseased patient - these models should show the expected altered gene expression (e.g., increase or decrease in fxnexpression).
  • All references, patents or applications, U.S. or foreign, cited in the application are hereby incorporated by reference as if written herein in their entireties. Where any inconsistencies arise, material literally disclosed herein controls.
  • From the foregoing description, one skilled in the art can easily ascertain the essential characteristics of this disclosure, and without departing from the spirit and scope thereof, can make various changes and modifications of the disclosure to adapt it to various usages and conditions.
  • The following numbered paragraphs set out preferred features and preferred combinations of features of the present invention:
    1. A transcription modulator molecule having a first terminus, a second terminus, and an oligomeric backbone, wherein:
    1. a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to a nucleotide repeat sequence GAA;
    2. b) the second terminus comprises a protein-binding moiety binding to a regulatory molecule that modulates an expression of a gene comprising the nucleotide repeat sequence GAA; and
    3. c) the oligomeric backbone comprising a linker between the first terminus and the second terminus, with the proviso that the second terminus is not a Brd4 binding moiety.
    2. The transcription modulator molecule of para 1, wherein the first terminus comprises a polyamide selected from the group consisting of a linear polyamide, a hairpin polyamide, a H-pin polyamide, an overlapped polyamide, a slipped polyamide, a cyclic polyamide, a tandem polyamide, and an extended polyamide.
    3. The transcription modulator molecule of para 1 or 2, wherein the first terminus comprises a linear polyamide.
    4. The transcription modulator molecule of para 1 or 2, wherein the first terminus comprises a hairpin polyamide.
    5. The transcription modulator molecule of any one of paras 2-4, wherein the polyamide is capable of binding the DNA with an affinity of less than 500 nM.
    6. The transcription modulator molecule of any one of paras 1-5, wherein the first terminus comprises -NH-Q-C(O)-, wherein Q is an optionally substituted C6-10 arylene, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene group.
    7. The transcription modulator molecule of any one of paras 1-6, wherein the first terminus comprises at least three heteroaromatic carboxamide moieties comprising at least one heteroatom selected from O, N, and S, and at least one aliphatic amino acid residue chosen from the group consisting of glycine, β-alanine, γ-aminobutyric acid, 2,4-diaminobutyric acid, and 5-aminovaleric acid.
    8. The transcription modulator molecule of para 7, wherein the heteroaromatic carboxamide moiety is a monocyclic or bicyclic moiety.
    9. The transcription modulator molecule of para 7, wherein the first terminus comprises one or more carboxamide moieties selected from the group consisting of optionally substituted pyrrole carboxamide monomer, optionally substituted imidazole carboxamide monomer, and β-alanine monomer.
    10. The transcription modulator molecule of any one of paras 7-9, wherein the carboxamide moieties are selected based on the pairing principle shown in Table 1A, Table 1B, Table 1C, or Table 1D.
    11. The transcription modulator molecule of any one of paras 1-10, wherein the first terminus comprises Im corresponding to the nucleotide G, Py or β corresponding to the nucleotide pair C, Py or β corresponding to the nucleotide pair A, Py, β, or Hp corresponding to the nucleotide T, and wherein Im is N-C1-6alkyl imidazole, Py is N-C1-6alkyl pyrrole, Hp is 3 -hydroxy N-C1-6alkyl pyrrole, and β-alanine.
    12. The transcription modulator molecule of any one of paras 1-10, wherein the first terminus comprises Im/Py to correspond to the nucleotide pair G/C, Py/Im to correspond to the nucleotide pair C/O, Py/Py to correspond to the nucleotide pair A/T, Py/Py to correspond to the nucleotide pair T/A, Hp/Py to correspond to the nucleotide pair T/A, and wherein Im is N-C1-6alkyl imidazole, Py is N-C1-6alkyl pyrrole, and Hp is 3 -hydroxy N-C1-6alkyl pyrrole.
    13. The transcription modulator molecule of any one of paras 1-12, wherein the first terminus comprises a structure of Formula (A-1):

            -L1a-[A-M]p-E1 (     A-1)

    wherein:
    • each [A-M] appears p times and p is an integer in the range of 1 to 10;
    • L1a is a bond, a C1-6 alkylene, -NRa-C1-6 alkylene-C(O)-, -NRC(O)-, -NRa-C1-6 alkylene, -O-, or -O-C1-6 alkylene;
    • each A is selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-,-CONRa-,-CONRaC1-aalkylene-, -NR-CO-C1-4alkylene-, -C(O)O-, -O-, -S-, -S(O)-, -S(O)2-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene,
      Figure imgb0475
       -NH-C1-6 alkylene-NH-, -O-C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof and at least one A is -CONH-;
    • each M is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • E1 is H or -AE-G;
    • AE is absent or -NHCO-;
    • G is selected from the group consisting of optionally substituted H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)-(NRaRb), -C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH)Ra, and optionally substituted amine; and
    • each Ra and Rb are independently selected from the group consisting of H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl,
    optionally substituted 4-10 membered heterocyclyl, and optionally substituted 5-10 membered heteroaryl.
    14. The transcription modulator molecule of any one of paras 1-12, wherein the first terminus comprises a structure of Formula (A-2):
    Figure imgb0476
     wherein:
    • L2a is a linker selected from -C1-12 allcyleno-CRa, -CH, N, -C1-6 alkylene-N, -C(O)N, -NRa-C1-6 alkylene-CH, -O-C0-6 alkylene-CH, ,
      Figure imgb0477
      Figure imgb0478
    • each p and q are independently an integer in the range of 1 to 10;
    • each m and n are independently an integer in the range of 0 to 10;
    • each A is independently selected from a bond, C1-10 alkylene, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4 alkylene-, -C(O)O-, -O-, -S-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, or -C(O)-CH=CH-, and at least one A is -CONH-;
    • each M is independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each E1 and E2 are independently H or -AE-G,
    • each AE is independently absent or NHCO,
    • G is selected from the group consisting of H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb), C1-5alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine; and
    • each Ra and Rb are independently selected from the group consisting of H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, and an optionally substituted 5-10 membered heteroaryl; and
    • each R1a and R1b is independently H, or C1-6 alkyl.
    15. The transcription modulator molecule of para 14, wherein integers p and q are 2≦p+q≦20.
    16. The transcription modulator molecule of para 14 or 15, wherein L2a is-C2-8 alkylene-CH,
    Figure imgb0479
     and wherein each m and n is independently an integer in the range of 0 to 10.
    17. The transcription modulator molecule of any one of paras 1-12, wherein the first terminus comprises a structure of Formula (A-3):

            -L1a-[A-M]p1-L3a-[M-A]q1-E1     (A-3)

    wherein:
    • L1a is a bond, a C1-6 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, or -O-C0-6 alkylene;
    • L3a is a bond, C1-6 alkylene, -NH-C0.6 alkylene-C(O)-, -N(CH3)-C0.6 alkylene, -O-C0-6 alkylene, -(CH2)a-NRa-(CH2)b-, -(CH2)a-, -(CH2)a-O-(CH2)b-, -(CH2)a-CH(NHRa)-, -(CH2)a-CH(NHRa)-, -(CR1aR1b)a-, or -(CH2)a-CH(NRaRb)-(CH2)b-;
    • each a and b are independently an integer between 2 and 4;
    • each Ra and Rb are independently selected from H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, and an optionally substituted 5-10 membered heteroaryl;
    • each R1a and R1b is independently H, halogen, OH, NHAc, or C1-4 alkyl;
    • each [A-M] appears p1 times and p1 is an integer in the range of 1 to 10;
    • each [M-A] appears q1 times and q1 is an integer in the range of 1 to 10;
    • each A is selected from a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, -R-CO-C1-4alkylene-, -C(O)O-, -O-, -S-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene,
      Figure imgb0480
       -NH-C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof and at least one A is -CONH-;
    • each M in each [A-M] and [M-A] unit is independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene; and
    • E1 is selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaR2), -C0-4alkylene-C(=N+H2)(NRaRb), -C1-5 alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine.
    18. The transcription modulator molecule of any one of paras 13 to 17, when M is a 10 membered bicyclic aryle or heteroaryl ring, at least one A adjacent to M is a bond.
    19. The transcription modulator molecule of 18, wherein M is anthracene or benzimidazole.
    20. The transcription modulator molecule of any one of paras 13 to 17, wherein one A is a 4-10 membered heterocyclyl or 5-10 membered heteraryl having at least one nitrogen, optioanlly substituted by one or more groups selected from oxo and C1-6 alkyl.
    21. The transcription modulator molecule of any one of paras 13 to 17, wherein at least one A is a triazole or a 4-10 membered heterocyclyl having a cyclic amide or cyclic amine.
    22. The transcription modulator molecule of any one of paras 13 to 17, wherein integers p1 and q1 are 2≦p1+q1≦20.
    23. The transcription modulator molecule of any one of paras 1-12, wherein the first terminus comprises a structure of Formula (A-4a) or (A-4b):
    Figure imgb0481
     Or
    Figure imgb0482
     wherein:
    • L1c is a bivalent or trivalent group selected from
      Figure imgb0483
      Figure imgb0484
       a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
      Figure imgb0485
    • p is an integer in the range of 2 to 10;
    • p' is an integer in the range of 2 to 10; 2 ≦ q ≦ p − 1 ;
      Figure imgb0486
       2 ≦ r ≦ p − 1 ;
      Figure imgb0487
    • m and n are each independently an integer in the range of 0 to 10;
    • each A2 through Ap is independently selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, - C1-10alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, -C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-,-C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene, and
      Figure imgb0488
       -NH-C1-6 alkylene-NH-, -0- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof and at least one of A2 through Ap is -CONH-;
    • each M1 through Mp is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each T2 through Tp' in formula (A-4a) is independently selected from the group consisting of a bond, C1-10 alkylene, optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NRa-, -CO-, -NRa-, -CONRa-,-CONRaC1-4alkylene-, - NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, -C(=S)-NH, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, (CH2)0-4-CH=CH-(CH2)0-4, -N(CH3)-C1-6 alkylene, and
      Figure imgb0489
       NH- C1-6 alkylene-NH-, -O- C1-6 alkylene-O-, -NH-N=N-, -NH-C(O)-NH-, and any combinations thereof and at least one of T2 through Tp is -CONH-;
    • each Q1 to Qp' is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each A1, T1, E1, and E2 are independently H or -AE-G,
    • each AE is independently absent or NHCO,
    • each G is independently selected from the group consisting of optionally substituted H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb), -C1-5 alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, and optionally substituted amine;
    • when L1c is a trivalent group, the oligomeric backbone is attached to the first terminus through L1c, when L1c is a bivalent group, the oligomeric backbone is attached to the first terminus through one of A1, T1, E1, and E2, or the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of M1, M2, ...Mp-1, Mp, T1, T2, ...Tp'-1, and Tp', and
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl;
    • each R1a and R1b are independently H or an optionally substituted C1-6 alkyl.
    24. The transcription modulator molecule of para 23, wherein when one of M1 through Mp or M1 through Mp is a 10 membered bicyclic aryl or heteroaryl ring, the adjacent A or T is a bond.
    25. The transcription modulator molecule of para 23 or 24, wherein L1c is
    Figure imgb0490
     C1-10 alkylene, or
    Figure imgb0491
     26. The transcription modulator molecule of any one of paras 23 to 25, wherein L1c is
    Figure imgb0492
     and wherein 2≦m+n≦10.
    27. The transcription modulator molecule of 26, wherein 3≦m+n≦7.
    28. The transcription modulator molecule of 23, wherein L1c is C3-8 alkylene.
    29. The transcription modulator molecule of any one of paras 23 to 28, wherein Mq is a five membered heteroaryl ring comprising at least one nitrogen; Qq is a five membered heteroaryl ring comprising at least one nitrogen; L1c is linked to the nitrogen atom on Mq and L1c is linked to the nitrogen atom on Qq.
    30. The transcription modulator molecule of any one of paras 23 to 29, wherein each M1 through Mp is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C1-6 alkylene.
    31. The transcription modulator molecule of any one of paras 23 to 30, wherein each Q1 to Qp' is independently selected from an optionally substituted pyrrolylene, an optionally substituted imidazolylene, an optionally substituted pyrazolylene, an optionally substituted thioazolylene, an optionally substituted diazolylene, an optionally substituted benzopyridazinylene, an optionally substituted benzopyrazinylene, an optionally substituted phenylene, an optionally substituted pyridinylene, an optionally substituted thiophenylene, an optionally substituted furanylene, an optionally substituted piperidinylene, an optionally substituted pyrimidinylene, an optionally substituted anthracenylene, an optionally substituted quinolinylene, and an optionally substituted C1-6 alkylene.
    32. The transcription modulator molecule of any one of paras 23 to 31, wherein each A2 through Ap is independently selected from a bond, C1-10 alkylene, optionally substituted phenylene, optionally substituted thiophenylene, optionally substituted furanylene, optionally substituted triazole, a 4-10 membered heterocyclyl having a cyclic amide, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NH-, -CO-, - NRa-, -CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, - C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, -CH=CH-, -NH-N=N-, -NH-C(O)-NH-, -N(CH3)-C1-6 alkylene, and
    Figure imgb0493
     -NH- C1-6 alkylene-NH-, -O-C1-6 alkylene-O-, and any combinations thereof.
    33. The transcription modulator molecule of any one of paras 23 to 32, wherein each T2 through Tp' is independently selected from a bond, C1-10 alkylene, optionally substituted phenylene, optionally substituted thiophenylene, optionally substituted furanylene, optionally substituted triazole, a 4-10 membered heterocyclyl having a cyclic amide, -C1-10 alkylene-C(O)-, -C1-10 alkylene-NH-, -CO-, - NRa-, -CONRa-,-CONRaC1-4alkylene-, -NRaCO-C1-4alkylene-, -C(O)O-, -O-, -S-, - C(=S)-NH-, -C(O)-NH-NH-, -C(O)-N=N-, -C(O)-CH=CH-, -CH=CH-, -NH-N=N-, -NH-C(O)-NH-, -N(CH3)-C1-6 alkylene, and
    Figure imgb0494
     -NH- C1-6 alkylene-NH-, -O-C1-6 alkylene-O-, and any combinations thereof.
    34. The transcription modulator molecule of any one of paras 23 to 33, wherein each G is an end group independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, a 5-10 membered heteroaryl optionally substituted with 1-3 substituents selected from C1-6 alkyl, -NHCOH, halogen, -NRaRb, , an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, C0-4 alkylene-NHC(=NH)-RE, -C1-4 alkylene-, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb)C1-5 alkylene-NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine.
    35. The transcription modulator molecule of any one of paras 23 to 34, wherein each G is independently selected from C1-4alkylNHC(NH)NH2,
    Figure imgb0495
     -C(=NH)(NH2),
    Figure imgb0496
    Figure imgb0497
    Figure imgb0498
    Figure imgb0499
    Figure imgb0500
    Figure imgb0501
    Figure imgb0502
     36. The transcription modulator molecule of any one of paras 13-15, wherein each E1 independently comprises an optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted imidazole containing moiety, or optionally substituted amine.
    37. The transcription modulator molecule of para 14, wherein each E2 independently comprises an optionally substituted thiophene-containing moiety, optionally substituted pyrrole containing moiety, optionally substituted imidazole containing moiety, or optionally substituted amine.
    38. The transcription modulator molecule of para 18 or 37, wherein each E1 and E2 are independently selected from the group consisting of optionally substituted N-methylpyrrole, optionally substituted N-methylimidazole, optionally substituted benzimidazole moiety, and optionally substituted 3-(dimethylamino)propanamidyl.
    39. The transcription modulator molecule of para 38, wherein each E1 and E2 independently comprises thiophene, benzothiophene, C-C linked benzimidazole/thiophene-containing moiety, or C-C linked hydroxybenzimidazole/thiophene-containing moiety.
    40. The transcription modulator of para 38 or 39, wherein each E1 or E2 are independently selected from the group consisting of isophthalic acid; phthalic acid; terephthalic acid; morpholine; N,N-dimethylbenzamide; N,N-bis(trifluoromethyl)benzamide; fluorobenzene; (trifluoromethyl)benzene; nitrobenzene; phenyl acetate; phenyl 2,2,2-trifluoroacetate; phenyl dihydrogen phosphate; 2H-pyran; 2H-thiopyran; benzoic acid; isonicotinic acid; and nicotinic acid; wherein one, two, or three ring members in any of the end-group candidates can be independently substituted with C, N, S or O; and where any one, two, three, four or five of the hydrogens bound to the ring can be substituted with R3a , wherein R5 may be independently selected from H, OH, halogen, C1-10 alkyl, NO2, NH2, C1-10 haloalkyl, -OC1-10 haloalkyl, COOH, and CONR1cR1d; wherein each R1c and R1d are independently H, C1-10 alkyl, C1-10 haloalkyl, or -C1-10 alkoxyl.
    41. The transcription modulator molecule of para any one of paras 1-12, wherein the first terminus comprises the structure of Formula (A-5a) or Formula (A-Sb);

            A1a-NH-Q1-C(O)-NH-Q2-C(O)-NH-Q3-C(O)... -NH-Qp-1C(O)-NH-C(O)NH-G     (Formula A-5a)

    or

            T1a-C(O)-Q1-NH-C(O)-Q2NH-C(O)-Q3-NH-... -C(O)-Qp-1NH-C(O)-Qp-NHC(O)-G     (Formula A-5b)

    wherein:
    • each Q1, Q2, Q3... through Qp are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each A1a and T1a are independently a H, bond, a -C1-6 alkylene-, -NH-C0-6 alkylene-C(O)-, - N(CH3)-C0-6 alkylene, -C(O)-, -C(O)-C1-10alkylene, and -O-C0-6 alkylene, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), C0-4alkylene-C(=N+H2)(NRaRb)C1-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine;
    • p is an integer between 2 and 10; and
    • G is selected from the group consisting of an optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, or an optionally substituted alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb), -C1-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine;
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl; and
    • wherein the first terminus is connected to the oligomeric backbone through either A1 or T1, or through a nitrogen or carbon atom on one of Q1 through Qp.
    42. The transcription modulator molecule of para any one of paras 1-12, wherein the first terminus comprises the structure of Formula (A-5c) or (A-5d):
    Figure imgb0503
     or
    Figure imgb0504
     wherein:
    • each Qa 1, Qa 2...Qa q...through Qa p are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • each Qb 1,Qb 2...Qb r....through Qb p' are independently an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or an optionally substituted alkylene;
    • p and p' are independently an integer between 3 and 10; 2 ≦ q ≦ p − 1 ;
      Figure imgb0505
       2 ≦ r ≦ p − 1 ;
      Figure imgb0506
    • La is selected from a divalent or trivalent group selected from the group consisting of
      Figure imgb0507
      Figure imgb0508
       a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
      Figure imgb0509
    • each m and n are independently an integer in the range of 1 to 10;
    • n is an integer in the range of 1 to 10;
    • each R1a and R1b are independently H, or C1-6 alkyl;
    • each Wa 1, Ga, Gb, and Wb 1 are and groups independently selected from the group consisting of optionally substituted H, C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, C0-4 alkylene-NHC(=NH)NH, -CN, -C0-4alkylene-C(=NH)(NRaRb), -C0-4alkylene-C(=N+H2)(NRaRb), -C1-5alkylene- NRaRb, C0-4 alkylene-NHC(=NH) Ra, -CO-halogen, and optionally substituted amine;
    • when La is a trivalent group, the oligomeric backbone is attached to the first terminus through La; and when La is a divalent group, the oligomeric backbone is attached to the first terminus through one of Wa 1, E., Eb, and Wb 1, or the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of Qa 1, Qa 2, ... Qa p-1, Qa p, Qb 1, Qa 2, ... Qb p'-1, and Qb p'; and
    • each Ra and Rb are independently H, an optionally substituted C1-6 alkyl, an optionally substituted C3-10 cycloalkyl, optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, or an optionally substituted 5-10 membered heteroaryl.
    43. The transcription modulator molecule of para 42, wherein L, is
    Figure imgb0510
     or a C2-8 alkylene.
    44. The transcription modulator molecule of para any one of paras 1-41, wherein the first terminus comprises at least one C3-5 achiral aliphatic or heteroaliphatic amino acid.
    45. The transcription modulator molecule of para 44, wherein the first terminus comprises one or more subunits selected from the group consisting of optionally substituted pyrrole, optionally substituted imidazole, optionally substituted thiophene, optionally substituted furan, optionally substituted beta-alanine, γ-aminobutyric acid, (2-aminoethoxy)-propanoic acid, 3((2-aminoethyl)(2-oxo-2-phenyl-1λ2-ethyl)amino)-propanoic acid, anddimethylaminopropylamide monomer.
    46. The transcription modulator molecule of any one of paras 1-12, wherein the first terminus comprises a polyamide having the structure of Formula (A-6):
    Figure imgb0511
     wherein:
    • each A1 is -NH- or -NH-(CH2)m-CH2-C(O)-NH-;
    • each M1 is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocyclene, optionally substituted 5-10 membered heteroarylene group, or optionally substituted alkylene;
    • m is an integer between 1 to 10; and
    • n is an integer between 1 and 6.
    47. The transcription modulator molecule as recited in any one of paras 1-12 and 46, wherein the first terminus has the structure of Formula (A-7):
    Figure imgb0512
     or a salt thereof, wherein:
    • E is an end subunit which comprises a moiety chosen from a heterocyclic group or a straight chain aliphatic group, which is chemically linked to its single neighbor;
    • X1, Y1, and Z1 in each m1 unit are independently selected from CR4, N, NR5, O, or S;
    • X2, Y2, and Z2 in each m3 unit are independently selected from CR4, N, NR5, O, or S;
    • X3, Y3, and Z3 in each m5 unit are independently selected from CR4, N, NR5, O, or S;
    • X4, Y4, and Z4 in each m7 unit are independently selected from CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, or C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl, or C1-6 alkylamine;
    • each m1, m3, m5 and m7 are independently an integer between 0 and 5;
    • each m2, m4 and m6 are independently an integer between 0 and 3; and m1 + m2 + m3+ m4+ m3+ m6+ m7 is between 3 and 15.
    48. The transcription modulator molecule as recited in any one of paras 1-12 and 46, wherein the first terminus has the structure of Formula (A-8):
    Figure imgb0513
     or a salt thereof, wherein:
    • E is an end subunit which comprises a moiety chosen from a heterocyclic group or a straight chain aliphatic group, which is chemically linked to its single neighbor;
    • W is C1-6 alkylene,
      Figure imgb0514
    • X1', Y1', and Z1' in each n1 unit are independently selected from CR4, N, NR5, O, or S;
    • X2', Y2', and Z2' in each n3 unit are independently selected from CR4, N, NR5, O, or S;
    • X3', Y3', and Z3' in each n5 unit are independently selected from CR4, N, NR5, O, or S;
    • X4', Y4', and Z4' in each n6 unit are independently selected from CR4, N, NR5, O, or S;
    • X5', Y5', and Z5' in each n8 unit are independently selected from CR4, N, NR5, O, or S;
    • X6', Y6', and Z6' in each n10 unit are independently selected from CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl or C1-6alkylamine;
    • n is an integer between 1 and 5;
    • each n1, n3, n5, n6, n8 and n10 are independently an integer between 0 and 5;
    • each n2, n4, n7 and n9 are independently an integer between 0 and 3, and
    • n1 + n2 + n3+ n4+ n5+ n6+ n7+ n8+ n9+ n10 is between 3 and 15.
    49. The transcription modulator molecule as recited in any one of paras 1-12 and 46, wherein the first terminus has the structure of Formula (A-9):
    Figure imgb0515
     or a salt thereof, wherein:
    • X1', Y1', and Z1' in each n1 unit are independently selected from CR4, N, NR5, O, or S;
    • X2', Y2', and Z2' in each n3 unit are independently selected from CR4, N, NR5, O, or S;
    • X3', Y3', and Z3' are independently selected from CR4, N, NR5, O, or S;
    • X4', Y4', and Z4' in each n6 unit are independently selected from CR4, N, NR5, O, or S;
    • X5', Y5', and Z5' in each n8 unit are independently selected from CR4, N, NR5, O, or S;
    • X6', Y6', and Z6' in each n9 unit are independently selected from CR4, N, NR5, O, or S;
    • X7', Y7', and Z7' in each n11 unit are independently selected from CR4, N, NR5, O, or S;
    • X8', Y8', and Z8' are independently selected from CR4, N, NR5, O, or S;
    • X9', Y9', and Z9' in each n14 unit are independently selected from CR4, N, NR5, O, or S;
    • X10', Y10', and Z10' in each n16 unit are independently selected from CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl or C1-6alkylamine;
    • each n1, n3, n6, n8, n9, n11, n14, and n16 are independently an integer between 0 and 5;
    • each n2, n4, n5, n7, n10, n13, and n13 are independently an integer between 0 and 3,
    • n1 + n2 + n3+ n4+ n5+ n6+ n7+ n8+ n9+ n10+n11+ n12+n13+n14+n15+ n16 is between 3 and 18 or a salt thereof, wherein:
      • La is selected from a divalent or trivalent group selected from the group consisting of
        Figure imgb0516
        Figure imgb0517
         a C1-10 alkylene, -NH-C0-6 alkylene-C(O)-, -N(CH3)-C0-6 alkylene, and
        Figure imgb0518
      • each R1a and R1b are independently H, or an C1-6 alkyl;
      • each m and n are independently an integer between 1 and 10;
      • each E1a, E2a, E1b, and E2b are end groups independently selected from the group consisting of optionally substituted C6-10 aryl, optionally substituted 4-10 membered heterocyclyl, optionally substituted 5-10 membered heteroaryl, an optionally substituted C1-6 alkyl, and optionally substituted amine;
    • when La is a trivalent group, the oligomeric backbone is attached to the first terminus through La;
    • when La is a divalent group, the oligomeric backbone is attached to the first terminus through one of E1a, E2a, E1b, and F2b, or the oligomeric backbone is attached to the first terminus through a nitrogen or carbon atom on one of five-membered heteroaryl rings.
    50. The transcription modulator molecule of any one of paras 1-12 and 46, wherein the first terminus comprises a polyamide having the structure of Formula (A-10):
    Figure imgb0519
     wherein:
    • each Y1, Y2, Z1, and Z2 are independently CR4, N, NR5, O, or S;
    • each R4 is independently H, -OH, halogen, C1-6 alkyl, or C1-6 alkoxyl;
    • each R5 is independently H, C1-6 alkyl, or C1-6 alkylamine;
    • each W1 and W2 are independently a bond, NH, C1-6 alkylene, -NH-C1-6 alkylene, -NH-5-10 membered heteroarylene, -NH-5-10 membered heterocyclene, -N(CH3)-C0-6 alkylene, -C(O)-C1-10 alkylene, or -O-C0-6 alkylene; and
    • n is an integer between 2 and 11.
    51. The transcription modulator molecule of any one of paras 47-50, wherein R4 is selected from the group consisting of H, COH, Cl, NO, N-acetyl, benzyl, C1-6 alkyl, C1-6 alkoxyl, C1-6 alkenyl, C1-6 alkynyl , C1-6 alkylamine, -C(O)NH-(CH2)1-4-C(O)NH -(CH2)1-4-NRaRb; and each Ra and Rb are independently hydrogen or C1-6 alkyl.
    52. The transcription modulator molecule of any one of paras 47-50, wherein R5 is independently selected from the group consisting of H, C1-6 alkyl, and C1-6 alkylNH2, preferably H, methyl, or isopropyl.
    53. The transcription modulator molecule of any one of paras 1-52, wherein the first terminus comprises a polyamide having one or more subunits independently selected from
    Figure imgb0520
    Figure imgb0521
    Figure imgb0522
    Figure imgb0523
    Figure imgb0524
    Figure imgb0525
    Figure imgb0526
    Figure imgb0527
     -NH-benzopyrazinylene-CO-, -NH-phenylene-CO-, -NH-pyridinylene-CO-, -NH-piperidinylene-CO-, -NH-pyrimidinylene-CO-, -NH-anthracenylene-CO-, -NH-quinolinylene-CO-, and
    Figure imgb0528
     wherein Z is H, NH2, C1-6 alkyl, C1-6 haloalkyl or C1-6 alkyl-NH2.
    54. The transcription modulator molecule of para 53, wherein Py is
    Figure imgb0529
     Im is
    Figure imgb0530
     Hp is
    Figure imgb0531
     Th is
    Figure imgb0532
     Pz is
    Figure imgb0533
     Nt is
    Figure imgb0534
     Tn is
    Figure imgb0535
     Nh is
    Figure imgb0536
     iNt is
    Figure imgb0537
     is
    Figure imgb0538
     HpBi is
    Figure imgb0539
     ImBi is
    Figure imgb0540
     PyBi is
    Figure imgb0541
     Dp is
    Figure imgb0542
     -NH-benzopyrazinylene-CO- is
    Figure imgb0543
     -NH-phenylene-CO- is
    Figure imgb0544
     -NH-pyridinylene-CO- is
    Figure imgb0545
     -NH-piperidinylene-CO- is
    Figure imgb0546
     -NH-pyrazinylene-CO- is
    Figure imgb0547
     -NH-anthracenylene-CO- is
    Figure imgb0548
     and -NH-quinolinylene-CO- is
    Figure imgb0549
     55. The transcription modulator molecule of para 53, wherein the first terminus comprises one or more subunits selected from the group consisting of optionally substituted N-methylpyrrole, optionally substituted N-methylimidazole, and β-alanine (β).
    56. The transcription modulator molecule of any one of paras 1-55, wherein the first terminus does not have thestructure of
    Figure imgb0550
     57. The transcription modulator molecule of any one of paras 1-56, wherein the linker has a length of less than about 50 Angstroms.
    58. The transcription modulator molecule of any one of paras 1-57, wherein the linker has a length of about 20 to 30 Angstroms.
    59. The transcription modulator molecule of any one of paras 1-58, wherein the linker comprises between 5 and 50 chain atoms.
    60. The transcription modulator molecule of any one of paras 1-59, wherein the linker comprises a multimer having from 2 to 50 spacing moieties, and wherein the spacing moiety is independently selected from the group consisting of -((CR3aR3b)x-O)y-, -((CR3aR3b)xNR4a)y-, -((CR3aR3b)x-CH=CH-(CR3aR3b)x-O)y-, optionally substituted -C1-12 alkyl, optionally substituted C2-10 alkenyl, optionally substituted C2-10 alkynyl, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, optionally substituted 4- to 10-membered heterocycloalkylene, an amino acid residue, -O-, -C(O)NR4a-, -NR4aC(O)-, -C(O)-, -NR4a-,-C(O)O-,-O-, -S-, -S(O)-, -SO2-, -SO2NR4a-, -NR4aSO2-, and -P(O)OH-, and any combinations thereof, wherein
    • each x is independently 2-4;
    • each y is independently 1-10;
    • each R3a and R3b are independently selected from hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, optionally substituted alkylamide, sulfonyl, optionally substituted thioalkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted cycloalkyl, and optionally substituted heterocyclyl; and
    • each R4a is independently a hydrogen or an optionally substituted C1-6 alkyl.
    61. The transcription modulator molecule of any one of paras 1-60, wherein the oligomeric backbone comprises -(T1-V1)a-(T2-V2)b-(T3-V3)c-(T4-V4)d-(T5-V5)e-,
    • wherein a, b, c, d and e are each independently 0 or 1, and where the sum of a, b, c, d and e
      is 1 to 5;
    • T1, T2, T3, T4 and T5 are each independently selected from an optionally substituted (C1-C12) alkylene, optionally substituted alkenylene, optionally substituted alkynylene, (EA)w, (EDA)m, (PEG)n, (modified PEG)n, (AA)p, -(CR2aOH)h-, optionally substituted (C6-C10) arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10 membered heteroarylene, optionally substituted 4- to 10-membered heterocycloalkylene, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, and an ester;
    • each m, p, and w are independently an integer from 1 to 20;
    • n is an integer from 1 to 30;
    • h is an integer from 1 to 12;
    • EA has the following structure:
      Figure imgb0551
    • EDA has the following structure:
      Figure imgb0552
      • wherein each q is independently an integer from 1 to 6;
      • each x is independently an integer from 2 to 4 and
      • each r is independently 0 or 1;
    • (PEG)n has the structure of -(CR2aR2b-CR2aR2b-O)n-CR2aR2b-;
    • (modified PEG)n has the structure of replacing at least one -(CR2aR2b-CR2aR2b-O)- in (PEG)n with -(CH2-CR2a=CR-CH2-O)- or -(CR2aR2b-CR2aR2b-S)-;
    • AA is an amino acid residue;
    • V1, V2, V3, V4 and V5 are each independently selected from the group consisting of a bond, - CO-, -NR1a-, -CONR1a-, -NR1a-CO-, -CONR1aC1-4 alkyl-, -NR1aCO-C1-4 alkyl-, -C(O)O-, OC(O)-, - O-, -S-, -S(O)-, -SO2-, -SO2NR1a-, -NR1aSO2- and -P(O)OH-;
    • each R1a is independently hydrogen or and optionally substituted C1-6 alkyl; and each R2a and R2b are independently selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, halogen, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl.
    62. The transcription modulator molecule of para 61, wherein T1, T2, T3, T4, and T5 are each independently selected from (C1-C12)alkyl, substituted (C1-C12)alkyl, (EA)w, (EDA)m, (PEG)n, (modified PEG)n, (AA)p, -(CR2aOH)h-, an optionally substituted phenyl, piperidin-4-amino (P4A), piperidine-3-amino, piperazine, pyrrolidin-3-amino, azetidine-3-amino, para-amino-benzyloxycarbonyl (PABC), meta, amino-benzyloxycarbonyl (MABC), para-amino-benzyloxy (PABO), meta-amino-benzyloxy (MABO), para-aminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA)p-MABC-(AA)p, (AA)p-MABO-(AA)p, (AA)p-PABO-(AA)p and (AA)p-PABC-(AA)p.
    63. The transcription modulator molecule of para 62, wherein piperidin-4-amino (P4A) is
    Figure imgb0553
     wherein R1a is H or C1-6 alkyl.
    64. The transcription modulator molecule of para 61, wherein T1, T2, T3, T4 and T5 are each independently selected from (C1-C12)alkyl, substituted (C1-C12)alkyl, (EA)w, (EDA)m, (PEG)n, (modified PEG)n, (AA)p,-(CR2aOH)h-, optionally substituted (C6-C10) arylene, 4-10 membered heterocycloalkene, and optionally substituted 5-10 membered heteroarylene.
    65. The transcription modulator molecule of para 61, wherein T4 or T5 is an optionally substituted (C6-C10) arylene.
    66. The transcription modulator molecule of para 61, wherein T4 or T5 is an optionally substituted phenylene.
    67. The transcription modulator molecule of para 1, wherein T1, T2, T3, T4 and T3; and V1, V2, V3, V4 and V5 are selected from the following Table:
    T1 V1 T2 V2 T3 V3 T4 V4 T5 V5
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n NR11CO - ---- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O arylene NR11CO ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O Subst arylene NR11CO ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O NR11C O (C1-C12) alkyl Subst. arylene NR11CO
    (C1-C12) alkylene CONR1a (EA)w CO (C1-C12) alkyl NR11CO-C1-4 alkyl Subst arylene NR11 ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n O Subst arylene --- ---- ----
    (PEG)n CONR1a-C1-4 alkyl ---- ---- ---- ---- ---- ---- ---- ---
    (EA), CO (C1-C12) alkyl CONR11- C1-4 alkyl ---- ---- ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (EA)w CO (PEG)n NR11CO-C1-4 alkyl ---- ---- ---- ----
    (EA)w CO (PEG)n O phenyl NR11CO-C1-4 alkyl ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (PEG)n CO ---- ---- ---- ---- ---- ----
    (C1-C12) alkylene CONR1a (EA), CO modifd. (PEG)n O arylene NR11CO ---- ----
    wherein R1a is H or C1-6 alkyl, and n is an integer between 1 and 15.
    68. The transcription modulator molecule of any one of paras 1-67, wherein the linker comprises
    Figure imgb0554
     or any combination thereof, wherein r is an integer between 1 and 10, preferably between 3 and 7; X is O, S, or NR1a; and R1a is H or C1-6 alkyl.
    69. The transcription modulator molecule of any one of paras 1-68, wherein the linker comprises
    Figure imgb0555
     wherein at least one -(CH2-CH2-O)- is replaced with -((CR1aR1b)x-CH=CH-(CR1aR1b)x -O)-, or any combinations thereof, wherein W' is absent, (CH2)1-5, -(CH2)1-5O, (CH2)1-5-C(O)NH-(CH2)1-5-O, (CH2)1-5-C(O)NH-(CH2)1-5, -(CH2)1-5NHC(O)-(CH2)1-5-O, or -(CH2)1-5-NHC(O)-(CH2)1-5-; E3 is an optionally substituted C6-10 arylene group, optionally substituted 4-10 membered heterocycloalkylene, or optionally substituted 5-10 membered heteroarylene; X is O, S, or N; each R1a and R1b are independently H or C1-6 alkyl; r is an integer between 1 and 10; and x is an integer between 1 and 15.
    70. The transcription modulator molecule of para 69, wherein E3 is a phenylene or substituted phenylene.
    71. The transcription modulator molecule of para 69, wherein the linker comprises
    Figure imgb0556
     72. The transcription modulator molecule of any one of paras 1-69, wherein the linker comprises -X(CH2)m(CH2CH2O)n-, wherein X is -O-, -NH-, or -S-;m is 0 or greater; and n is at least 1.
    73. The transcription modulator molecule of any one of paras 1-69, wherein the linker comprises
    Figure imgb0557
     following the second terminus, wherein Rc is selected from a bond, -N(R1a)-, -O-, and -S-; Rd is selected from -N(R1a)-, -O-, and -S-; Re is independently selected from hydrogen and optionally substituted C1-6 alkyl; and R1a is H or C1-6 alkyl.
    74. The transcription modulator molecule of any one of paras 1-69, wherein the linker comprises one or more structures selected from
    Figure imgb0558
     -C1-12 alkyl, arylene, cycloalkylene, heteroarylene, heterocycloalkylene, -O-, -C(O)NR1a-,-C(O)-, -NR1a-, -(CH2CH2CH2O)y-, and -(CH2CH2CH2NR1a)y- wherein each d and y are independently 1-10, andeach R1a is independently hydrogen or C1-6 alkyl.
    75. The transcription modulator molecule of para 74, wherein the linker comprises
    Figure imgb0559
     , wherein d is 3-7.
    76. The transcription modulator molecule of any one of paras 1-75, wherein the linker comprises -N(R1a)(CH2)xN(R1b)(CH2)xN-, wherein R1a andR1b are each independently selected from hydrogen or optionally substituted C1-C6 alkyl; and each x is independently an integer in the range of 1-6.
    77. The transcription modulator molecule of any one of paras 1-76, wherein the linker comprises -(CH2 -C(O)N(R")-(CH2)q-N(R')-(CH2)q-N(R")C(O)-(CH2)x-C(O)N(R")-A-, -(CH2)x-C(O)N(R")-(CH2 CH2O)y(CH2) x -C(O)N(R")-A-, -C(O)N(R")-(CH2)q-N(R')-(CH2)q-N(R")C(O)-(CH2)x-A-, -(CH2)x-O-(CH2 CH2O)y-(CH2)x-N(R")C(O)-(CH2)x-A-, or -N(R")C(O)-(CH2)-C(O)N(R")-(CH2)x-O(CH2CH2O)y(CH2)x-A-; wherein R' is methyl; R" is hydrogen; each x and y are independently an integer from 1 to 10; each q is independently an integer from 2 to 10; and each A is independently selected from a bond, an optionally substituted C1-12 alkyl, an optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene.
    78. The transcription modulator molecule of any one of paras 1-77, wherein the linker is joined with the first terminus with a group selected from -CO-, -NR1a-,-CONR1a-, -NR1aCO-, -CONR1aC1-4alkyl-, - NR1aCO-C1-4alkyl-, -C(O)O-, -OC(O)-, -O-, -S-, -S(O)-, -SO2-, -SO2NR1a-, -NR1aSO2-, -P(O)OH-,-((CH2)x-O)-, -((CH2)y-NR1a)-, optionally substituted -C1-12 alkylene, optionally substituted C2-10 alkenylene, optionally substituted C2-10 alkynylene, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene; wherein each x and y are independently 1-4, and each R1a is independently a hydrogen or optionally substituted C1-6 alkyl.
    79. The transcription modulator molecule of any one of paras 1-78, wherein the linker is joined with the first terminus with a group selected from -CO-, -NR1a-, C1-12 alkyl, -CONR1a-, and -NR1aCO-; wherein each R1a is independently a hydrogen or optionally substituted C1-6 alkyl.
    80. The transcription modulator molecule of any one of paras 1-79, wherein the linker is joined with second terminus with a group selected from -CO-, -NR1a-,-CONR1a-, -NR1aCO-, -CONR1aC1-4alkyl-, - NR1-CO-C1-4alkyl-, -C(O)O-, -OC(O)-, -O-, -S-, -S(O)-, -SO2-, -SO2NR1a-, -NR1a-SO2-, -P(O)OH-,-((CH2)x-O)-, -((CH2)y-NR1a)-, optionally substituted -C1-12 alkylene, optionally substituted C2-10 alkenylene, optionally substituted C2-10 alkynylene, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene, wherein each x and y are independently 1-4, and each R1a is independently a hydrogen or optionally substituted C1-6 alkyl.
    81. The transcription modulator molecule of para 80, wherein the linker is joined with second terminus with a group selected from -CO-, -NR1a-, -CONR1a-, -NR1aCO-,-((CH2)x-O)-, -((CH2)y-NR1a)-, -O-, optionally substituted -C1-12 alkyl, optionally substituted C6-10 arylene, optionally substituted C3-7 cycloalkylene, optionally substituted 5- to 10-membered heteroarylene, and optionally substituted 4- to 10-membered heterocycloalkylene, wherein each x and y are independently 1-4, and each R1a is independently a hydrogen or optionally substituted C1-6 alkyl.
    82. The transcription modulator molecule of any one of paras 1-80, wherein the second terminus comprises one or more optionally substituted C6-10 aryl, optionally substituted C4-10 carbocyclic, optionally substituted 4 to 10 membered heterocyclic, or optionally substituted 5 to 10 membered heteroaryl.
    83. The transcription modulator molecule of any one of paras 1-82, wherein the protein binding moiety that binds to the regulatory molecule is selected from the group consisting of a CREB binding protein (CBP), a P300, an O-linked β-N-acetylglucosamine-transferase- (OGT-), a P300-CBP-associated-factor- (PCAF-), histone methyltransferase, histone demethylase, chromodomain, a cyclin-dependent-kinase-9- (CDK9-), a nucleosome-remodeling-factor-(NURF-), a bromodomain-PHD-finger-transcription-factor- (BPTF-), a ten-eleven-translocation-enzyme- (TET-), a methylcytosine-dioxygenase- (TET1-), histone acetyltransferase (HAT), a histone deacetalyse (HDAC), a host-cell-factor-1(HCF1-), an octamer-binding-transcription-factor- (OCT1-), a P-TEFb-, a cyclin-T1-, a PRC2-, a DNA-demethylase, a helicase, an acetyltransferase, a histone-deacetylase, and methylated histone lysine protein.
    84. The transcription modulator molecule of para 83, wherein the second terminus comprises a moiety that binds to an O-linked β-N-acetylglucosamine-transferase(OGT), or CREB binding protein (CBP).
    85. The transcription modulator molecule of para 83, wherein the protein binding moiety is a residue of a compound that binds to an O-linked β-N-acetylglucosamine-transferase(OGT), or CREB binding protein (CBP).
    86. The transcription modulator molecule of para 1, wherein the protein binding moiety is a residue of a compound selected from Table 2.
    87. The transcription modulator molecule of any one of paras 1-85, wherein the second terminus binds the regulatory molecule with an affinity of less than 200 nM.
    88. The transcription modulator molecule of any one of paras 1-86, wherein the protein binding moiety is a residue of a compound having a structure of Formula (C-1):
    Figure imgb0560
     wherein:
    • Xa is -NHC(O)-, -C(O)-NH-, -NHSO2-, or -SO2NH-;
    • Aa is selected from an optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl;
    • Xb is a bond, NH, NH-C1-10alkylene, -C1-12 alkyl, NHC(O)-, or -C(O)-NH-;
    • Ab is selected from an optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 4- to 10-membered heterocycloalkyl; and
    • each R1e, R2e, R3e, R4e are independently selected from the group consisting of H, OH, - NO2, halogen, amine, COOH, COOC1-10alkyl, -NHC(O)-optionally substituted -C1-12 alkyl, - NHC(O)(CH2)1-4NRfRg, -NHC(O)(CH2)0-4 CHRf(NRfRg), -NHC(O)(CH2)0-4 CHRfRg, - NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to10-membered heteroaryl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 4- to 10-membered heterocycloalkyl; and
    • wherein each Rfand Rg are independently H or C1-6 alkyl.
    89. The transcription modulator molecule of para 88, wherein the protein binding moiety is a residue of a compound having a structure of Formula (C-2):
    Figure imgb0561
     wherein R5e is independently selected from the group consisting of H, COOC1-10alkyl,-NHC(O)-optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkylsubstituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl.
    90. The transcription modulator molecule of para 88, wherein Aa is selected from an optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl.
    91. The transcription modulator molecule of para 88, wherein Aa is an optionally substituted C6-10 aryl.
    92. The transcription modulator molecule of para 88, wherein the protein binding moiety is a residue of a compound having a structure of Formula (C-3):
    Figure imgb0562
     wherein:
    • M1c is CR2h or N; and
    • each R1h, R2h, R3h, R4h, and R5h are independently selected from the group consisting of H, OH, -NO2, halogen, amine, COOH, COOC1-10alkyl, -NHC(O)-optionally substituted -C1-12 alkyl, - NHC(O)(CH2)1-4NRfRs, -NHC(O)(CH2)0-4 CHRf(NRfRg), -NHC(O)(CH2)0-4 CHRfRg, - NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to10-membered heteroaryl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl, wherein each Rf and Rg are independently H or C1-6 alkyl.
    93. The transcription modulator molecule of para 92, wherein each R1hand R5h are independently hydrogen, halogen, or C1-6 alkyl.
    94. The transcription modulator molecule of para 92, wherein each R2h and R3h are independently H, OH, -NO2, halogen, C1-4 haloalkyl, amine, COOH, COOC1-10alkyl, -NHC(O)-optionally substituted -C1-12 alkyl, -NHC(O)(CH2)1-4NR'R", -NHC(O)(CH2)0-4 CHR'(NR'R"), -NHC(O)(CH2)0-4 CHRfRg, -NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, - (CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to10-membered heteroaryl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl.
    95. The transcription modulator molecule of para 87, wherein Aa is a C6-10 aryl substituted with 1-4 substituents, and each substituent is independently selected from halogen, OH, NO2, an optionally substituted -C1-12 alkyl, optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10 membered heteroaryl, and optionally substituted 5-to 10-membered heterocycloalkyl.
    96. The transcription modulator molecule of para 87, wherein R1e, R3e, and R4e are hydrogen.
    97. The transcription modulator molecule of para 87, wherein R2e is selected from the group consisting of H, OH, -NO2, halogen, amine, COOH, COOC1-10alkyl, -NHC(O)-optionally substituted -C1-12 alkyl, -NHC(O)(CH2)1-4NRfRg, -NHC(O)(CH2)0-4 CHR'(NR'R"), -NHC(O)(CH2)0-4 CHRfRg, - NHC(O)(CH2)0-4-C3-7 cycloalkyl, -NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- to 10-membered heteroaryl, optionally substituted -C1-12 alkyl, -optionally substituted -C2-10 alkenyl, optionally substituted -C2-10 alkynyl, optionally substituted -C1-12 alkoxyl, optionally substituted -C1-12 haloalkyl, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, and optionally substituted 5- to 10-membered heterocycloalkyl, wherein each Rf and Rg are independently H or C1-6 alkyl.
    98. The transcription modulator molecule of para 87, wherein R2e is an phenyl or pyridinyl optionally substituted with 1-3 substituents, wherein the substituent is independently selected from the group consisting of OH, -NO2, halogen, amine, COOH, COOC1-10alkyl, NHC(O) -C1-12 alkyl, -NHC(O)(CH2)1-4NRfRg, -NHC(O)(CH2)0-4 CHRf (NRfRg), -NHC(O)(CH2)0-4 CHRfRg, -NHC(O)(CH2)0-4-C3-7 cycloalkyl,-NHC(O)(CH2)0-4-5- to 10-membered heterocycloalkyl, NHC(O)(CH2)0-4C6-10 aryl, -NHC(O)(CH2)0-4-5- to10-membered heteroaryl, -(CH2)1-4-C3-7 cycloalkyl, -(CH2)1-4-5- to 10-membered heterocycloalkyl, -(CH2)1-4C6-10 aryl, -(CH2)1-4-5- tolO-membered heteroaryl, -C1-12 alkoxyl, C1-12 haloalkyl, C6-10 aryl, C3-7 cycloalkyl, 5- to 10-membered heteroaryl, and 5- to 10-membered heterocycloalkyl, wherein each Rf and Rg are independently H or C1-6 alkyl.
    99. The transcription modulator of any one of paras 1-87, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-4):
    Figure imgb0563
     wherein:
    • R1c is an optionally substituted C6-10 aryl or an optionally substituted 5- to 10-membered heteroaryl,
    • Xc is -C(O)NH-, -C(O), -S(O2)-, -NH-, or -C1-4alkyl-NH,
    • n is 0-10,
    • R2j is -NR3jR4j, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, or optionally substituted 4- to 10-membered heterocycloalkyl; and
    • each R3j and R4j are independently H or optionally substituted -C1-12 alkyl.
    100. The transcription modulator molecule of para 99, wherein R2j is -NHC(CH3)3, or a 4- to 10-membered heterocycloalkyl substituted with C1-12 alkyl.
    101. The transcription modulator of any one of paras 1-87, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-5):
    Figure imgb0564
     wherein:
    • X2c is a bond, C(O), SO2, or CHR3c;
    • M2c is CH or N;
    • n is 0-10,
    • R2j is -NR3jR4j, optionally substituted C6-10 aryl, optionally substituted C3-7 cycloalkyl, optionally substituted 5- to 10-membered heteroaryl, or optionally substituted 4- to 10-membered heterocycloalkyl;
    • each R5j is independently -NR3jR4j, -C(O)R3j, -COOH, -C(O)NHC1-6alkyl, an optionally substituted C6-10 aryl, or an optionally substituted 5- to 10-membered heteroaryl;
    • R6j is -NR3jR4j, -C(O)R3j, an optionally substituted C6-10 aryl, or an optionally substituted 5-to 10-membered heteroaryl; and
    • each R3j and R4j are independently H, an optionally substituted C6-10 aryl, optionally substituted 4- to 10-membered heterocycloalkyl, or optionally substituted -C1-12 alkyl.
    102. The transcription modulator molecule of para 101, wherein R2j is a 4- to 10-membered heterocycloalkyl substituted by a 4- to 10-membered heterocycloalkyl.
    103. The transcription modulator molecule of para 101, wherein R6j is -C(O)R3j, and R3j is a 4-to 10-membered heterocycloalkyl substituted by a 4- to 10-membered heterocycloalkyl.
    104. The transcription modulator molecule of para 101, wherein each R5j is independently H, - C(O)R3j, -COOH, -C(O)NHC1-6alkyl, -NH-C6-10 aryl, or optionally substituted C6-10 aryl.
    105. The transcription modulator molecule of any one of paras 1-75, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-6):
    Figure imgb0565
     wherein:
    • X3c is a bond, NH, C1-4 alkylene, or NC1-4 alkyl;
    • R7j is an optionally substituted C1-6 alkyl, an optionally substituted cyclic amine, an optionally substituted aryl, an optionally substituted 5- to 10-membered heteroaryl, or optionally substituted 4- to 10-membered heterocycloalkyl,
    • R8j is H, halogen, or C1-6 alkyl; and
    • R9j is H, or C1-6 alkyl.
    106. The transcription modulator molecule of para 100, wherein R7j is an optionally substituted cyclic secondary or tertiary amine.
    107. The transcription modulator molecule of para 100, wherein R7j is a tetrahydroisoquinoline optionally substituted with C1-4 alkyl.
    108. The transcription modulator molecule of any one of paras 1-75, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-7):
    Figure imgb0566
     wherein:
    • A1a is an optionally substituted aryl or heteroaryl;
    • X2 is a bond, (CH2)1-4, or NH; and
    • A2a is an optionally substituted aryl, heterocyclic, or heteroaryl, linked to an amide group.
    109. The transcription modulator molecule of para 108, wherein A1a is an aryl substituted with one or more halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, or C1-6 haloalkyl.
    110. The transcription modulator molecule of para 108, wherein X2 is NH.
    111. The transcription modulator molecule of para 108, wherein A2a is a heterocyclic group.
    112. The transcription modulator molecule of para 108, wherein A2a is a pyrrolidine.
    113. The transcription modulator molecule of para 108, wherein A2a is an optionally substituted phenyl.
    114. The transcription modulator molecule of para 108, wherein A2a is a phenyl optionally substituted with one or more halogen, C1-6 alkyl, hydroxyl, C1-6 alkoxy, or C1-6 haloalkyl.
    115. The transcription modulator molecule of any one of paras 1-87, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-8):
    Figure imgb0567
     wherein R1k is H or C1-25 alkyl and R2k is OH or -OC1-12 alkyl.
    116. The transcription modulator molecule of any one of paras 1-87, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-9):
    Figure imgb0568
    • wherein R1m is H, OH, -CONH2, -COOH, -NHC(O)-C1-6 alkyl,-NHC(O)O-C1-6 alkyl,-NHS(O)2-C1- 6alkyl, -C1-6 alkyl, -C1-6 alkoxyl, or -NHC(O)NH-C1-6alkyl;
    • R2m is H, CN, or CONH2; and
    • R3m is an optionally substituted C6-10 aryl.
    117. The transcription modulator molecule of any one of paras 1-87, wherein the protein binding moiety is a residue of a compound having the structure of Formula (C-10):
    Figure imgb0569
    • wherein R1n is an optionally substituted C6-10 aryl or optionally substituted 5- to 10-membered heteroaryl, and
    • each R2n and R3n are independently H, -C1-4 alkyl-C6-10 aryl, -C1-4alkyl-5-to10-membered heteroaryl, C6-10 aryl, or -5-tolO-membered heteroaryl, or
    • R2n and R3n together with N form an optionally substituted 4-10 membered heterocyclic or heteroaryl group.
    118. The transcription modulator molecule of any one of paras 1-87, wherein the methylated histone lysine protein is selected from Ankyrin repeats, WD-40 repeat domains, MBT, Tudor, PWWP, chromodomain plant homeodomain (PHD) fingers, and ADD.
    119. The transcription modulator molecule of any one of paras 1-87, wherein the second terminus comprises at least one 5-10 membered heteroaryl group having at least two nitrogen atoms.
    120. The transcription modulator molecule of any one of paras 1-119, wherein the second terminus comprises a moiety capable of binding to the regulatory protein, and the moiety is from a compound capable of binding to the regulatory protein.
    121. The transcription modulator molecule of any one of paras 1-87, wherein the second terminus comprises at least one group selected from an optionally substituted diazine, an optionally substituted diazepine, and an optionally substituted phenyl.
    122. The transcription modulator molecule of any one of paras 1-121, wherein the second terminus does not comprises JQ1, iBET762, OTX015, RVX208, or AU1.
    123. The transcription modulator molecule of any one of paras 1-122, wherein the second terminus does not comprises JQ1.
    124. The transcription modulator molecule of any one of paras 1-123, wherein the second terminus does not comprises a moiety that binds to a bromodomain protein.
    125. The transcription modulator molecule of any one of paras 1-87, wherein the second terminus comprises a diazine or diazepine ring, wherein the diazine or diazepine ring is fused with a C6-10 aryl or a 5-10 membered heteroaryl ring comprising one or more heteroatom selected from S, N and O.
    126. The transcription modulator molecule of any one of paras 1-87, wherein the second terminus comprises an optionally substituted bicyclic or tricyclic structure.
    127. The transcription modulator molecule of para 126, wherein the optionally substituted bicyclic or tricyclic structure comprises a diazepine ring fused with a thiophene ring.
    128. The transcription modulator molecule of para 126, wherein the second terminus comprises an optionally substituted bicyclic structure, wherein the bicyclic structure comprises a diazepine ring fused with a thiophene ring.
    129. The transcription modulator molecule of para 126, wherein the second terminus comprises an optionally substituted tricyclic structure, wherein the tricyclic structure is a diazaphine ring that is fused with a thiophene and a triazole.
    130. The transcription modulator molecule of any one of paras 1-87, wherein the second terminus comprises an optionally substituted diazine ring.
    131. The transcription modulator molecule of any one of paras 1-130, wherein the second terminus does not comprise a structure of Formula (C-11):
    Figure imgb0570
     wherein:
    • each of A1p and B1p is independently an optionally substituted aryl or heteroaryl ring;
    • X1p is CH or N;
    • R1p is hydrogen, halogen, or an optionally substituted C1-6 alkyl group; and
    • R2p is an optionally substituted C1-6 alkyl, cycloalkyl, C6-10 aryl, or heteroaryl.
    132. The transcription modulator molecule of para 131, wherein X1p is N.
    133. The transcription modulator molecule of para 131, wherein A1p is an aryl or heteroaryl substituted with one or more substituents.
    134. The transcription modulator molecule of para 131, wherein A1p is an aryl or heteroaryl substituted with one or more substituents selected from halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, and C1-6haloalkyl.
    135. The transcription modulator molecule of para 131, wherein B1p is an optionally substituted aryl or heteroaryl substituted with one or more substituents selected from halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, and C1-6haloalkyl.
    136. The transcription modulator molecule of para 131, wherein A1p is an optionally substituted thiophene or phenyl.
    137. The transcription modulator molecule of para 131, wherein A1p is a thiophene or phenyl, each substituted with one or more substituents selected from halogen, C1-6 alkyl, hydroxyl, C1-6 alkoxy, and C1-6 haloalkyl.
    138. The transcription modulator molecule of para 131, wherein B1p is an optionally substituted triazole.
    139. The transcription modulator molecule of para 131, wherein B1p is a triazole substituted with one or more substituents selected from halogen, C1-6alkyl, hydroxyl, C1-6alkoxy, and C1-6haloalkyl.
    140. The transcription modulator molecule of any one of paras 1-139, wherein the protein binding moiety is not
    Figure imgb0571
    Figure imgb0572
     141. The transcription modulator molecule of any one of paras 1-140, wherein the protein binding moiety is not
    Figure imgb0573
     142. The transcription modulator molecule of any one of paras 1-139, wherein the protein binding moiety does not have the structure ofFormula (C-12):
    Figure imgb0574
     wherein:
    • R1q is a hydrogen or an optionally substituted alkyl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, halogenated alkyl, hydroxyl, alkoxy, or -COOR4q;
    • R4q is hydrogen, or an optionally substituted aryl, aralkyl, cycloalkyl, heteroaryl, heteroaralkyl, heterocycloalkyl, alkyl, alkenyl, alkynyl, or cycloalkylalkyl group, optionally containing one or more heteroatoms;
    • R2q is an optionally substituted aryl, alkyl, cycloalkyl, or aralkyl group;
    • R3q is hydrogen, halogen, or an optionally substituted alkyl group, preferably (CH2)x - C(O)N(R20)(R21), or (CH2)x-N(R20)-C(O)R21; or halogenated alkyl group;
    • wherein x is an integer from 1 to 10; and R20 and R21 are each independently hydrogen or C1-C6 alkyl group, preferably R20 is hydrogen and R21 ismethyl; and
    • Ring E is an optionally substituted aryl or heteroaryl group.
    143. A transcription modulator molecule as recited in any one of the proceeding paras for use as a medicament.
    144. A transcription modulator molecule as recited in any one of the proceeding paras for use in the manufacture of a medicament for the prevention or treatment of a disease or condition ameliorated by the overexpression of c9orj72.
    145. A transcription modulator molecule as recited in any one of the proceeding paras for use in the treatment of ALS.
    146. A pharmaceutical composition comprising a transcription modulator molecule as recited in any one of the proceeding paras and a pharmaceutically acceptable carrier.
    147. A method of modulation of the expression of c9orf72 comprising contacting c9orj72 with a transcription modulator molecule as recited in any one of paras 1-134.
    148. A method of treatment of a disease caused by expression of a defective c9orj72 comprising the administration of a therapeutically effective amount of a transcription modulator molecule as recited in any one of paras 1-134 to a patient in need thereof.
    149. The method as recited in para 148 wherein said disease is ALS.
    150. A method of treatment of a disease caused by expression of a defective c9orj72 comprising the administration of:
    • a therapeutically effective amount of a transcription modulator molecule as recited in any one of paras 1-130; and
    • another therapeutic agent.
    151. A method for achieving an effect in a patient comprising the administration of a therapeutically effective amount of a transcription modulator molecule as disclosed herein, or a salt thereof, to a patient, wherein the effect is chosen from muscular atrophy, ataxia, fasciculation, and dementia.
    152. A compound of structural Formula I:

            X-L-Y     (I)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • Y comprises a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the pentanucleotide repeat sequence GAA; and
    • L is a linker.
    153. The compound as recited in para 152, wherein
    • L comprises -(CH(CH3)OCH2)m-; and
    • m is an integer between 1 to 10, inclusive.
    154. The compound as recited in para 152, wherein the DNA recognition moiety Y comprises a polyamide sequence.
    155. The compound as recited in para 153, having structural Formula II:

            X-L-(Y1-Y2-Y3)n-Y0     (II)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • L is a linker;
    • Y1, Y2, and Y3 are internal subunits, each of which comprises a moiety chosen from a heterocyclic ring or a C1-6 straight chain aliphatic segment, and each of which is chemically linked to its two neighbors;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor;
    • each subunit can noncovalently bind to an individual nucleotide in the GAA repeat sequence;
    • n is an integer between 1 and 5, inclusive; and
    • (Y1-Y2-Y3)n-Y0 combine to form a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the hexanucleotide repeat sequence GAA.
    156. The compound as recited in para 155, wherein Y1, Y2, Y3, Y4, Y5, and Y6 each comprise a chemical moiety independently chosen from
    Figure imgb0575
    Figure imgb0576
    Figure imgb0577
    Figure imgb0578
     157. The compound as recited in para 152, having structural Formula III:

            X-L-(Y1-Y2-Y3)-W-(Y4-Y5-Y6)n-Y0     (III)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • L is a linker;
    • Y1, Y2, Y3, Y4, Y5, and Y6 are internal subunits, each of which comprises a moiety chosen from a heterocyclic ring or a C1-6 straight chain aliphatic segment, and each of which is chemically linked to its two neighbors;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor;
    • each subunit can noncovalently bind to an individual nucleotide in the GAA repeat sequence;
    • W is a spacer;
    • n is an integer between 1 and 5, inclusive; and
    • (Y1-Y2-Y3)-W-( Y4-Y5-Y6)n-Y0 combine to form a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the hexanucleotide repeat sequence GAA.
    158. The compound as recited in para 152, structural Formula IV:

            X-L-(Y1-Y2-Y3)-V-(Y4-Y5-Y6)-Y0     (IV)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • L is a linker chosen from a C1-6straight chain aliphatic segment and (CH2OCH2)m;
    • Y1, Y2, Y3, Y4, Y5, and Y6 are internal subunits, each of which comprises a moiety chosen from a heterocyclic ring or a C1-6straight chain aliphatic segment, and each of which is chemically linked to its two neighbors;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor;
    • each subunit can noncovalently bind to an individual nucleotide in the GAA repeat sequence;
    • V is a turn component for forming a hairpin turn; and
    • (Y1-Y2-Y3-)-V-(Y4-Y5-Y6)-Y0 combine to form a DNA recognition moiety that is capable of noncovalent binding to one or more copies of the hexanucleotide repeat sequence GAA.
    159. The compound as recited in para 152, having structural Formula V:

            X-C(=O)-CH2CH2-(Y1-Y2-Y3)n-NH-Y0     (V)

    or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus;
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; and n is an integer between 1 and 5, inclusive.
    160. The compound as recited in para 152, having structural VI:
    Figure imgb0579
     or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus; and
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; and
    • n is an integer between 1 and 5, inclusive.
    161. The compound as recited in para 152, having structural Formula VII:
    Figure imgb0580
     or a salt thereof, wherein:
    • X comprises a recruiting moiety that is capable of noncovalent binding to a regulatory molecule within the nucleus; and
    • W is a spacer; and
    • Y0 is an end subunit which comprises a moiety chosen from a heterocyclic ring or a straight chain aliphatic segment, which is chemically linked to its single neighbor; and
    • n is an integer between 1 and 5, inclusive.
    162. The compound as recited in para 152 for use in the treatment of ALS.
    163. The compound as recited in para 152, wherein A is selected from a bromodomain inhibitor, a BPTF inhibitor, a methylcytosine dioxygenase inhibitor, a DNA demethylase inhibitor, a helicase inhibitor, an acetyltransferase inhibitor, a histone deacetylase inhibitor, a CDK-9 inhibitor, a positive transcription elongation factor inhibitor, and a polycomb repressive complex inhibitor.
    164. The compound as recited in para 163, wherein A is selected from a bromodomain inhibitor and a CDK9 inhibitor.
    165. A compound as recited in para 152 for use as a medicament.
    166. A compound as recited in para 152 for use in the manufacture of a medicament for the prevention or treatment of a disease or condition ameliorated by the modulation of the expression of the fxn gene.
    167. A compound as recited in para 152 for use in the treatment of Friedreich's ataxia.
    168. A pharmaceutical composition comprising a compound as recited in para 1 together with a pharmaceutically acceptable carrier.
    169. A method of modulation of the expression of the fxn gene comprising contacting fxn with a compound as recited in para 152.
    170. A method of treatment of a disease associated with the expression of defective fxn comprising the administration of a therapeutically effective amount of a compound as recited in para 152 to a patient in need thereof.
    171. The method as recited in para 170 wherein said disease is Friedreich's ataxia.
    172. A method of treatment of a disease associated with the expression of fxn comprising the administration of
    • a therapeutically effective amount of a compound as recited in para 152; and
    • another therapeutic agent.
    173. The method as recited in para 172, wherein said other agent is chosen from riluzole (RILUTEK®) and edaravone (RADICAVA®).
    174. A method for achieving an effect in a patient comprising the administration of a therapeutically effective amount of a compound as disclosed herein, or a salt thereof, to a patient, wherein the effect is chosen from muscular atrophy, ataxia, fasciculations, and dementia.

Claims (16)

  1. An ex-vivo method for modulating transcription of a gene comprising a trinucleotide repeat sequence GAA the method comprising contacting a cell comprising the gene with an agent having a first terminus, a second terminus, and an oligomeric backbone, wherein:
    (a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to the trinucleotide repeat sequence GAA;
    (b) the second terminus comprises a protein-binding moiety capable of binding to a regulatory molecule that modulates an expression of the gene comprising the trinucleotide repeat sequence GAA; and
    (c) the oligomeric backbone comprises a linker between the first terminus and the second terminus; with the proviso that the second terminus is not a Brd4 binding moiety.
  2. An agent for use in a method of treatment of a disease, wherein the method comprises contacting a cell comprising a gene that comprises a trinucleotide repeat sequence GAA with the agent, wherein the agent modulates transcription of the gene,
    and wherein the agent has a first terminus, a second terminus, and an oligomeric backbone, wherein:
    (a) the first terminus comprises a DNA-binding moiety capable of noncovalently binding to the trinucleotide repeat sequence GAA;
    (b) the second terminus comprises a protein-binding moiety capable of binding to a regulatory molecule that modulates an expression of the gene comprising the trinucleotide repeat sequence GAA; and
    (c) the oligomeric backbone comprises a linker between the first terminus and the second terminus; with the proviso that the second terminus is not a Brd4 binding moiety.
  3. The method of claim 1 or agent for use of claim 2, wherein the DNA-binding moiety is a polyamide selected from of a linear polyamide, a hairpin polyamide, a H-pin polyamide, an overlapped polyamide, a slipped polyamide, a cyclic polyamide, a tandem polyamide, and an extended polyamide.
  4. The method of claim 1 or agent for use of claim 2, wherein the trinucleotide repeat comprises at least 20 repeats, at least 50 repeats, at least 100 repeats, at least 200 repeats, at least 500 repeats, or at least 1000 repeats.
  5. The method of claim 1 or agent for use of claim 2, wherein the protein-binding moiety is capable of binding to a regulatory molecule that is selected from the group consisting of a CREB binding protein (CBP), a P300, an O-linked β-N-acetylglucosamine-transferase (OGT), a P300-CBP-associated-factor (PCAF), a histone methyltransferase, a histone demethylase, a chromodomain, a cyclin-dependent-kinase-9 (CDK9), a nucleosomeremodeling-factor (NURF), a bromodomain-PHD-finger-transcription-factor (BPTF), a teneleven-translocation-enzyme (TET), a methylcytosine-dioxygenase (TET1), a histone acetyltransferase (HAT), a histone deacetylase (HDAC), a host-cell-factor-1 (HCF1), an octamer-binding-transcription-factor (OCTI), a P-TEFb, a cyclin-Tl, a PRC2, a DNAdemethylase, a helicase, an acetyltransferase, a histone-deacetylase, a bromodomaincontaining protein and a methylated histone lysine protein.
  6. The method of claim 1 or agent for use of claim 2, wherein the protein-binding moiety is selected from the group consisting of a bromodomain inhibitor, a BPTF inhibitor, a methylcytosine dioxygenase inhibitor, a DNA demethylase inhibitor, a helicase inhibitor, an acetyltransferase inhibitor, a histone deacetylase inhibitor, a CDK-9 inhibitor, a positive transcription elongation factor inhibitor, and a polycomb repressive complex inhibitor.
  7. The method of claim 1 or agent for use of claim 2, wherein the second terminus does not comprise a moiety that binds to a bromodomain protein.
  8. The method of claim 1 or agent for use of claim 2, wherein the protein-binding moiety does not comprise JQ1, iBET762, OTX015, RVX208, or AU1.
  9. The method of claim 1 or agent for use of claim 2, wherein the protein-binding moiety binds the regulatory molecule with an affinity of less than 200 nM.
  10. The method of claim 1 or agent for use of claim 2, wherein the linker has a length of less than about 50 Angstroms.
  11. The method of any one of claims 1 and 3-10 or agent for use of any one of claims 2-10, wherein the gene is FXN.
  12. The method or agent for use of claim 11, wherein the DNA-binding moiety is capable of selectively binding to a GAA trinucleotide repeat sequence of FXN.
  13. The method or agent for use of claim 11, wherein the method comprises decreasing FXN expression.
  14. The method or agent for use of claim 11, wherein the method comprises a 20%, 50%, 80%, 90%, 95%, or 99% decrease in expression of FXN.
  15. The agent for use of any one of claims 2-14, wherein the method further comprises treating a disease mediated by transcription of an allele of FXN comprising the GAA trinucleotide repeat sequence in a patient in need thereof.
  16. The agent for use of claim 15, wherein the disease is Friedreich's Ataxia (FA).
EP23160417.4A 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease Withdrawn EP4234550A3 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201862674968P 2018-05-22 2018-05-22
EP19730621.0A EP3797106A1 (en) 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease
PCT/US2019/033625 WO2019226836A1 (en) 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
EP19730621.0A Division EP3797106A1 (en) 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease

Publications (2)

Publication Number Publication Date
EP4234550A2 true EP4234550A2 (en) 2023-08-30
EP4234550A3 EP4234550A3 (en) 2023-09-06

Family

ID=66858011

Family Applications (2)

Application Number Title Priority Date Filing Date
EP23160417.4A Withdrawn EP4234550A3 (en) 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease
EP19730621.0A Withdrawn EP3797106A1 (en) 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease

Family Applications After (1)

Application Number Title Priority Date Filing Date
EP19730621.0A Withdrawn EP3797106A1 (en) 2018-05-22 2019-05-22 Methods and compounds for the treatment of genetic disease

Country Status (3)

Country Link
US (2) US20210228723A1 (en)
EP (2) EP4234550A3 (en)
WO (1) WO2019226836A1 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
TW202142261A (en) * 2020-02-03 2021-11-16 美商規劃醫療公司 Methods and compounds for the treatement of genetic disease
TW202413344A (en) * 2022-06-15 2024-04-01 美商規劃醫療公司 Methods and compounds for modulating inherited genetic diseases

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060270727A1 (en) * 2005-05-03 2006-11-30 Christian Melander Small molecule therapeutics and uses therefor
US10517877B2 (en) * 2016-03-30 2019-12-31 Wisconsin Alumni Research Foundation Compounds and methods for modulating frataxin expression

Non-Patent Citations (15)

* Cited by examiner, † Cited by third party
Title
B ZHU ET AL., BIOORG MED CHEM, vol. 23, no. 12, 2015, pages 2917 - 2927
BB LAO ET AL., PNAS USA, vol. 111, no. 21, 2014, pages 7531 - 7536
CHANG Y: "Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294", NATURE STRUCT. MOL. BIOL., vol. 16, 2009, pages 312 - 317
DUDLEY AM ET AL.: "Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range", PNAS USA, vol. 99, no. 11, 2002, pages 7554 - 7559, XP002338318, DOI: 10.1073/pnas.112683499
F MORALES ET AL.: "Overview of CDK9 as a target in cancer rese", CELL CYCLE, vol. 15, no. 4, 2016, pages 519 - 527, XP093032257, DOI: 10.1080/15384101.2016.1138186
F MORALES ET AL.: "Overview of CDK9 as a target in cancer research", CELL CYCLE, vol. 15, no. 4, 2016, pages 519 - 527, XP093032257, DOI: 10.1080/15384101.2016.1138186
FREEMAN WM ET AL.: "Quantitative RT-PCR: pitfalls and potential", BIOTECHNIQUES, vol. 26, 1999, pages 112 - 125
ITKONEN HM: "Inhibition of O-G!cNAc transferase activity reprograms prostate cancer cell metabolism", ONCOTARGET, vol. 7, no. 1 1, 2016, pages 12464 - 12476
ITKONEN HM: "Inhibition of O-GlcNAc transferase activity reprograms prostate cancer cell metabolism", ONCOTARGET, vol. 7, no. 11, 2016, pages 12464 - 12476
JI STUCKEY ET AL., NATURE CHEM BIOL, vol. 12, no. 3, 2016, pages 180 - 187
KD BARNASH ET AL., ACS CHEM. BIOL., vol. 1 1, no. 9, 2016, pages 2475 - 2483
KONZE KD, ACS CHEM BIOL, vol. 8, no. 6, 2013, pages 1324 - 1334
N. CAOY. HUANGJ. ZHENG: "Conversion of human fibroblasts into functional cardiomyocytes by small molecules", SCIENCE, vol. 352, no. 6290, 2016, pages 1216 - 1220, XP055366967, DOI: 10.1126/science.aaf1502
SORAGNI E, FRONT. NEUROL, vol. 6, 2015, pages 44
WANG Z ET AL.: "RNA-Seq: a revolutionary tool for transcriptomics", NATURE REV. GENETICS, vol. 10, 2009, pages 57 - 63, XP055152757, DOI: 10.1038/nrg2484

Also Published As

Publication number Publication date
US20240269290A1 (en) 2024-08-15
WO2019226836A1 (en) 2019-11-28
EP4234550A3 (en) 2023-09-06
US20210228723A1 (en) 2021-07-29
EP3797106A1 (en) 2021-03-31

Similar Documents

Publication Publication Date Title
EP4234553A2 (en) Methods and compounds for the treatment of genetic disease
EP3781160A1 (en) Methods and compounds for the treatment of genetic disease
US20240269290A1 (en) Methods and compounds for the treatment of genetic disease
US20240050576A1 (en) Methods and compounds for the treatment of genetic disease
EP3797105A1 (en) Methods and compounds for the treatment of genetic disease
US20230050819A1 (en) Methods and compounds for the treatment of genetic disease
US20240166693A1 (en) Methods and compounds for modulating myotonic dystropy 1
AU2022206424A1 (en) Methods and compounds for treating friedreich's ataxia
EP4257128A2 (en) Methods and compounds for the treatment of genetic disease
US20230285569A1 (en) Methods and compounds for the treatment of fragile x
AU2023205889A1 (en) Compounds and methods for treating friedreich's ataxia
US20240042046A1 (en) Methods and compounds for modulating huntington's disease

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION HAS BEEN PUBLISHED

PUAL Search report despatched

Free format text: ORIGINAL CODE: 0009013

AC Divisional application: reference to earlier application

Ref document number: 3797106

Country of ref document: EP

Kind code of ref document: P

AK Designated contracting states

Kind code of ref document: A2

Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

AK Designated contracting states

Kind code of ref document: A3

Designated state(s): AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR

RIC1 Information provided on ipc code assigned before grant

Ipc: C12Q 1/6883 20180101ALI20230731BHEP

Ipc: A61K 31/4178 20060101ALI20230731BHEP

Ipc: A61P 25/28 20060101ALI20230731BHEP

Ipc: C07D 403/14 20060101ALI20230731BHEP

Ipc: C07D 403/12 20060101AFI20230731BHEP

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN

18D Application deemed to be withdrawn

Effective date: 20240307